[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/15078636/GBM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/15658343/transformed.cor.cli.txt"

nPatients in clinical file=592, in cluster file=283, common to both=278
[1]  38 278
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            78            200 
  TP53 MUTATED TP53 WILD-TYPE 
            78            200 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              32              246 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              32              246 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           23           255 
  RB1 MUTATED RB1 WILD-TYPE 
           23           255 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            85            193 
  PTEN MUTATED PTEN WILD-TYPE 
            85            193 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           29           249 
  NF1 MUTATED NF1 WILD-TYPE 
           29           249 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            264 
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            264 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              28              250 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              28              250 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             266 
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             266 
[1] "SEMG2 MUTATION ANALYSIS"
[1] 3
  SEMG2 MUTATED SEMG2 WILD-TYPE 
             11             267 
  SEMG2 MUTATED SEMG2 WILD-TYPE 
             11             267 
[1] "MAP3K1 MUTATION ANALYSIS"
[1] 3
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               6              272 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               6              272 
[1] "SLC26A3 MUTATION ANALYSIS"
[1] 3
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                6               272 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                6               272 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            16            262 
  ATRX MUTATED ATRX WILD-TYPE 
            16            262 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             6            272 
  BRAF MUTATED BRAF WILD-TYPE 
             6            272 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            73            205 
  EGFR MUTATED EGFR WILD-TYPE 
            73            205 
[1] "TMPRSS6 MUTATION ANALYSIS"
[1] 3
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                6               272 
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                6               272 
[1] "SEMA3C MUTATION ANALYSIS"
[1] 3
  SEMA3C MUTATED SEMA3C WILD-TYPE 
              11              267 
  SEMA3C MUTATED SEMA3C WILD-TYPE 
              11              267 
[1] "RPL5 MUTATION ANALYSIS"
[1] 3
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            271 
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            271 
[1] "PDGFRA MUTATION ANALYSIS"
[1] 3
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              12              266 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              12              266 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
              5             273 
  MMP13 MUTATED MMP13 WILD-TYPE 
              5             273 
[1] "REN MUTATION ANALYSIS"
[1] 3
  REN MUTATED REN WILD-TYPE 
            5           273 
  REN MUTATED REN WILD-TYPE 
            5           273 
[1] "DSP MUTATION ANALYSIS"
[1] 3
  DSP MUTATED DSP WILD-TYPE 
           10           268 
  DSP MUTATED DSP WILD-TYPE 
           10           268 
[1] "CHD8 MUTATION ANALYSIS"
[1] 3
  CHD8 MUTATED CHD8 WILD-TYPE 
             8            270 
  CHD8 MUTATED CHD8 WILD-TYPE 
             8            270 
[1] "KDR MUTATION ANALYSIS"
[1] 3
  KDR MUTATED KDR WILD-TYPE 
            8           270 
  KDR MUTATED KDR WILD-TYPE 
            8           270 
[1] "ODF4 MUTATION ANALYSIS"
[1] 3
  ODF4 MUTATED ODF4 WILD-TYPE 
             3            275 
  ODF4 MUTATED ODF4 WILD-TYPE 
             3            275 
[1] "TP63 MUTATION ANALYSIS"
[1] 3
  TP63 MUTATED TP63 WILD-TYPE 
             6            272 
  TP63 MUTATED TP63 WILD-TYPE 
             6            272 
[1] "PRKCD MUTATION ANALYSIS"
[1] 3
  PRKCD MUTATED PRKCD WILD-TYPE 
              3             275 
  PRKCD MUTATED PRKCD WILD-TYPE 
              3             275 
[1] "ACSM2B MUTATION ANALYSIS"
[1] 3
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               4              274 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               4              274 
[1] "CLCN7 MUTATION ANALYSIS"
[1] 3
  CLCN7 MUTATED CLCN7 WILD-TYPE 
              4             274 
  CLCN7 MUTATED CLCN7 WILD-TYPE 
              4             274 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             3            275 
  DDX5 MUTATED DDX5 WILD-TYPE 
             3            275 
[1] "FBN3 MUTATION ANALYSIS"
[1] 3
  FBN3 MUTATED FBN3 WILD-TYPE 
            11            267 
  FBN3 MUTATED FBN3 WILD-TYPE 
            11            267 
[1] "CD1D MUTATION ANALYSIS"
[1] 3
  CD1D MUTATED CD1D WILD-TYPE 
             4            274 
  CD1D MUTATED CD1D WILD-TYPE 
             4            274 
[1] "TEX15 MUTATION ANALYSIS"
[1] 3
  TEX15 MUTATED TEX15 WILD-TYPE 
              8             270 
  TEX15 MUTATED TEX15 WILD-TYPE 
              8             270 
[1] "KEL MUTATION ANALYSIS"
[1] 3
  KEL MUTATED KEL WILD-TYPE 
           15           263 
  KEL MUTATED KEL WILD-TYPE 
           15           263 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             21             257 
  MUC17 MUTATED MUC17 WILD-TYPE 
             21             257 
[1] "SLC6A14 MUTATION ANALYSIS"
[1] 3
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                5               273 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                5               273 
[1] "LRRC55 MUTATION ANALYSIS"
[1] 3
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               6              272 
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               6              272 
[1] "CD209 MUTATION ANALYSIS"
[1] 3
  CD209 MUTATED CD209 WILD-TYPE 
              5             273 
  CD209 MUTATED CD209 WILD-TYPE 
              5             273 
[1] "LZTR1 MUTATION ANALYSIS"
[1] 3
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             11             267 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             11             267 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "DCC_UPLOAD_DATE"                       
 [7] "GENDER"                                
 [8] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
 [9] "RADIATION_THERAPY"                     
[10] "KARNOFSKY_PERFORMANCE_SCORE"           
[11] "HISTOLOGICAL_TYPE"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 278 columns.

[1] "Batch" "15"   
[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=188,	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=227,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              17-7-2014 26-3-2015 6-11-2014
freq.values   "1"       "276"     "1"      
freq.contrast "277"     "2"       "277"    
both >= 3     "FALSE"   "FALSE"   "FALSE"  
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'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 9:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 278 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"                        
[2] "GENDER"                                
[3] "KARNOFSKY_PERFORMANCE_SCORE"           
[4] "HISTOLOGICAL_TYPE"                     
[5] "RADIATIONS_RADIATION_REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, 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    28  50
  TP53 WILD-TYPE  39 161
  TP53 MUTATED TP53 WILD-TYPE 
            78            200 
  TP53 MUTATED TP53 WILD-TYPE 
            50            161 
$`TP53 MUTATED`
TCGA-02-0003 TCGA-02-0033 TCGA-02-0055 TCGA-02-2483 TCGA-02-2485 TCGA-06-0128 
        4.73         2.83         2.50        15.32        15.45        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0184 TCGA-06-0188 TCGA-06-0189 TCGA-06-0195 
       33.67        12.95        69.90        44.58        15.42         7.40 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0644 TCGA-06-0743 TCGA-06-0744 
       13.64        13.32        48.69        12.62        26.40        46.88 
TCGA-06-0875 TCGA-06-0876 TCGA-06-2558 TCGA-06-2559 TCGA-06-2563 TCGA-06-2567 
       43.46        46.19        12.49         4.93        30.64         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5417 TCGA-06-5858 TCGA-06-6389 
        0.43        31.50        11.74         5.10         6.15         7.79 
TCGA-06-6694 TCGA-06-6698 TCGA-06-6701 TCGA-12-0618 TCGA-12-0619 TCGA-14-0740 
        7.36         4.77         4.96        12.99        34.92        11.97 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1456 TCGA-14-1825 TCGA-14-4157 
        1.35         5.39        28.93        40.96         7.63         3.42 
TCGA-15-1444 TCGA-16-0846 TCGA-19-1390 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 
       50.53         3.91        25.38         7.53         4.08        24.23 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5136 TCGA-27-1830 TCGA-27-1835 TCGA-27-1836 
       31.33        14.86        18.97         5.06        21.30        30.05 
TCGA-27-1838 TCGA-27-2519 TCGA-27-2521 TCGA-28-1753 TCGA-28-2509 TCGA-28-5207 
       11.51        10.39        10.39         1.22         4.77        11.28 
TCGA-28-5216 TCGA-28-5219 TCGA-32-1970 TCGA-32-2491 TCGA-32-2634 TCGA-32-4208 
       13.64        22.68        15.39        12.23        22.78        21.14 
TCGA-32-4210 TCGA-41-2575 TCGA-41-5651 TCGA-74-6573 TCGA-76-4925 TCGA-76-4929 
        3.72         9.53        15.12         3.45         4.80         3.65 
TCGA-76-4934 TCGA-76-6193 TCGA-76-6286 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        2.53         2.70        20.98         9.27         7.73         7.79 

$`TP53 WILD-TYPE`
TCGA-02-0047 TCGA-02-2470 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       14.73        12.92        20.32         2.70         6.15        20.38 
TCGA-06-0126 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
        6.94        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-06-0192 
        3.29         4.47         3.22        88.14        73.84        38.96 
TCGA-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0240 
        7.63         0.53        15.02        24.16         0.72        20.42 
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-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0877 TCGA-06-0878 
        7.86         2.70         2.70         0.92         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 
       40.41        16.57        20.78        26.76        13.61        15.32 
TCGA-06-2557 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-5410 
        1.08        17.65        12.56         5.95        16.64         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 
        8.35         4.54         8.81         8.98         8.55         2.73 
TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        3.75         4.57         5.23         5.39         1.48       120.56 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-08-0386 TCGA-12-0615 
        8.32        12.85         1.55         4.77        18.02        15.35 
TCGA-12-0616 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 
       14.73        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0862 
        0.95        23.05         2.24        11.24        13.78         2.89 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 
        0.79         1.38        58.78        17.85         7.17        17.49 
TCGA-14-3476 TCGA-15-0742 TCGA-16-0861 TCGA-16-1045 TCGA-19-1790 TCGA-19-2619 
        0.39        13.78         4.31        29.03         5.06         9.67 
TCGA-19-2620 TCGA-19-2624 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 
        4.87         0.16         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-26-5134 TCGA-26-5135 
       16.80        14.96        13.87         9.40         5.49         8.88 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        1.58         7.92         2.33        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1837 TCGA-27-2518 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       40.54        14.04        24.76        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-2499 TCGA-28-2502 TCGA-28-2513 
       14.40        15.78         2.53         3.12         0.66         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 TCGA-32-1977 
       23.44        11.01         5.16        12.76         5.42         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 
       19.50         1.18         4.67        12.69        16.93        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4209 TCGA-32-4211 
       15.02        15.95         8.84        25.18        20.32        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-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-74-6575 
        0.99         4.44        11.84         0.20        12.46        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-76-4931 TCGA-76-4932 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 
        9.17        47.93        10.78        16.70         3.29        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-81-5910 
       17.06         8.35         4.83         5.03         0.23         1.61 
TCGA-81-5911 TCGA-87-5896 
       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 
        12.100         10.535 
[1] "0.4 - 69.9 (12.1)"  "0.1 - 120.6 (10.5)"
[1] "hr=" "1.7"
D1V2, continuous
D1V3, binary
                cls
clus               0   1
  TP53 MUTATED    30  48
  TP53 WILD-TYPE  70 130
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     30   48
  TP53 WILD-TYPE   70  130
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           30             70
  MALE             48            130
[1] 2 2
[1] FALSE
D1V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  TP53 MUTATED                               1                   0
  TP53 WILD-TYPE                             8                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  TP53 MUTATED                                77
  TP53 WILD-TYPE                             188
D1V5, multiclass
                                 clus
vv                                TP53 MUTATED TP53 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              1              8
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM           77            188
[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"
D1V6, binary
                cls
clus               0   1
  TP53 MUTATED    57  21
  TP53 WILD-TYPE 129  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     57   21
  TP53 WILD-TYPE  129   71
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            57            129
  YES           21             71
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       2                         6    68
  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                               68            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  61
  TP53 WILD-TYPE   2 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   61
  TP53 WILD-TYPE    2  159
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           61            159
[1] 2 2
[1] FALSE

Clustering(2) Variable = PIK3R1 MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED     8  24
  PIK3R1 WILD-TYPE  59 187
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              32              246 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              24              187 
$`PIK3R1 MUTATED`
TCGA-02-0003 TCGA-06-0128 TCGA-06-0129 TCGA-06-0750 TCGA-06-0877 TCGA-06-2562 
        4.73        22.72        33.67         0.92         5.65        12.56 
TCGA-06-6388 TCGA-06-6695 TCGA-12-0688 TCGA-14-0790 TCGA-14-0862 TCGA-14-1456 
        5.23         8.32        26.66        13.78         2.89        40.96 
TCGA-15-1444 TCGA-19-2629 TCGA-19-5947 TCGA-19-5951 TCGA-19-5955 TCGA-19-5958 
       50.53        24.23         6.64         8.02         1.78        14.07 
TCGA-26-5139 TCGA-26-6174 TCGA-28-2513 TCGA-32-1991 TCGA-32-2634 TCGA-41-3915 
        1.58         2.33         7.30        16.93        22.78        11.84 
TCGA-74-6573 TCGA-74-6575 TCGA-76-4927 TCGA-76-4929 TCGA-76-6280 TCGA-76-6656 
        3.45        20.91        17.59         3.65        11.38         4.83 
TCGA-76-6657 TCGA-76-6662 
        5.03         9.27 

$`PIK3R1 WILD-TYPE`
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-06-0130 
       20.32         2.70         6.15        20.38         6.94        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-06-0209 TCGA-06-0213 TCGA-06-0214 
       15.42        38.96         7.40         7.63         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-06-0875 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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       26.76        13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        4.57         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
       12.85         4.77         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0692 TCGA-12-0821 
       15.35        14.73        12.99        34.92         3.65        10.62 
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-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 
       11.24         1.35         5.39        28.93         0.79         1.38 
TCGA-14-1450 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       58.78        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-15-0742 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 
        3.42        13.78         3.91         4.31        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-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        7.00         4.50        17.19        18.90         4.73        12.10 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-1442 TCGA-26-5132 TCGA-26-5133 
       16.80        14.96        13.87        31.33         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-6173 TCGA-27-1830 TCGA-27-1831 
        5.49         8.88        18.97         7.92         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        10.39        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 
        2.86        14.40        15.78         2.53         1.22         3.12 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        0.66         4.77         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-32-1970 TCGA-32-1977 
        5.16        22.68        12.76         5.42        15.39         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-2491 TCGA-32-2494 
       19.50         1.18         4.67        12.69        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 
       15.02        15.95         8.84        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-41-4097 
       13.35         8.94         9.53         0.99         4.44         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
       15.12        12.46         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         9.17        47.93         2.53        10.78 
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-76-6661 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        0.23         7.73         7.79         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 
           8.795           10.900 
[1] "0.9 - 50.5 (8.8)"   "0.1 - 120.6 (10.9)"
[1] "hr=" "1"  
D2V2, continuous
D2V3, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     9  23
  PIK3R1 WILD-TYPE  91 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      9   23
  PIK3R1 WILD-TYPE   91  155
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE              9               91
  MALE               23              155
[1] 2 2
[1] FALSE
D2V4, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PIK3R1 MUTATED                               1                   0
  PIK3R1 WILD-TYPE                             8                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  PIK3R1 MUTATED                                31
  PIK3R1 WILD-TYPE                             234
D2V5, multiclass
                                 clus
vv                                PIK3R1 MUTATED PIK3R1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                1                8
  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"
D2V6, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    23   9
  PIK3R1 WILD-TYPE 163  83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     23    9
  PIK3R1 WILD-TYPE  163   83
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO              23              163
  YES              9               83
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED       1                         2    27
  PIK3R1 WILD-TYPE     4                        15   223
D2V7, multiclass
                           clus
vv                          PIK3R1 MUTATED PIK3R1 WILD-TYPE
  ASIAN                                  1                4
  BLACK OR AFRICAN AMERICAN              2               15
  WHITE                                 27              223
[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   3 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      0   26
  PIK3R1 WILD-TYPE    3  194
                        clus
vv                       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             26              194
[1] 2 2
[1] FALSE

Clustering(3) Variable = RB1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     9  14
  RB1 WILD-TYPE  58 197
  RB1 MUTATED RB1 WILD-TYPE 
           23           255 
  RB1 MUTATED RB1 WILD-TYPE 
           14           197 
$`RB1 MUTATED`
TCGA-02-0033 TCGA-06-0130 TCGA-06-0140 TCGA-06-0184 TCGA-06-0188 TCGA-06-0195 
        2.83        12.95         0.20        69.90        44.58         7.40 
TCGA-06-0213 TCGA-06-0939 TCGA-06-5858 TCGA-06-6698 TCGA-19-2623 TCGA-19-2625 
        0.53        26.76         6.15         4.77         7.53         4.08 
TCGA-26-5132 TCGA-27-2524 TCGA-32-1970 TCGA-32-2491 TCGA-32-2632 TCGA-32-2634 
        9.40         7.59        15.39        12.23         8.84        22.78 
TCGA-32-4213 TCGA-76-6286 TCGA-76-6662 TCGA-76-6663 TCGA-81-5911 
       19.86        20.98         9.27         7.73        17.72 

$`RB1 WILD-TYPE`
TCGA-02-0003 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
        4.73        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-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 
       33.67        25.35        26.70        11.90        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-06-0185 TCGA-06-0189 TCGA-06-0192 
        4.47         3.22        88.14        73.84        15.42        38.96 
TCGA-06-0209 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        7.63        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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-1804 TCGA-06-1806 
        7.17        40.41        16.57        20.78        13.61        15.32 
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-06-5408 
        5.95        16.64         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        5.10         2.73         3.75         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 
        1.55         4.77         4.96        18.02        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 
       12.99        34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 
        2.04        11.97         0.95        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 
       13.78         1.35         5.39         2.89        28.93         0.79 
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-15-0742 TCGA-15-1444 TCGA-16-0846 
       17.49         0.39         3.42        13.78        50.53         3.91 
TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        4.31        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 
        0.16        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-26-1442 TCGA-26-5133 TCGA-26-5134 
       16.80        14.96        13.87        31.33        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        8.88        18.97         1.58         7.92         2.33         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        10.39        10.39        16.08 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 
        2.86        14.40        15.78         2.53         1.22         3.12 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         4.77         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-32-1977 
       13.64         5.16        22.68        12.76         5.42         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 
       19.50         1.18         4.67        12.69        16.93        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 
       15.02        15.95        25.18        21.14        20.32         3.72 
TCGA-32-4211 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       12.59        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-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
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        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       11.38        17.06         8.35         4.83         5.03         0.23 
TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 
        7.79         1.61        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 
         9.27         10.95 
[1] "0.2 - 69.9 (9.3)"   "0.1 - 120.6 (10.9)"
[1] "hr=" "1.3"
D3V2, continuous
D3V3, binary
               cls
clus              0   1
  RB1 MUTATED     7  16
  RB1 WILD-TYPE  93 162
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      7   16
  RB1 WILD-TYPE   93  162
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           7            93
  MALE            16           162
[1] 2 2
[1] FALSE
D3V4, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  RB1 MUTATED                               1                   0
  RB1 WILD-TYPE                             8                   4
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  RB1 MUTATED                                22
  RB1 WILD-TYPE                             243
D3V5, multiclass
                                 clus
vv                                RB1 MUTATED RB1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             1             8
  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"
D3V6, binary
               cls
clus              0   1
  RB1 MUTATED    16   7
  RB1 WILD-TYPE 170  85
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     16    7
  RB1 WILD-TYPE  170   85
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           16           170
  YES           7            85
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       0                         0    23
  RB1 WILD-TYPE     5                        17   227
D3V7, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            17
  WHITE                              23           227
[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  19
  RB1 WILD-TYPE   3 201
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   19
  RB1 WILD-TYPE    3  201
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          19           201
[1] 2 2
[1] FALSE

Clustering(4) Variable = PTEN MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    22  63
  PTEN WILD-TYPE  45 148
  PTEN MUTATED PTEN WILD-TYPE 
            85            193 
  PTEN MUTATED PTEN WILD-TYPE 
            63            148 
$`PTEN MUTATED`
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-06-5411 TCGA-06-5412 TCGA-06-5418 
        4.93        17.65        16.64         8.35         4.54         2.73 
TCGA-06-5858 TCGA-12-0618 TCGA-12-1597 TCGA-12-3649 TCGA-14-0781 TCGA-14-0813 
        6.15        12.99        22.19        15.22         0.95         1.35 
TCGA-14-1395 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-2625 TCGA-19-5952 
        1.38         3.91         4.31        29.03         4.08        18.90 
TCGA-19-5953 TCGA-19-5955 TCGA-19-5959 TCGA-26-5132 TCGA-26-6174 TCGA-27-1834 
        4.73         1.78        16.80         9.40         2.33        40.54 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-28-1753 
       14.04        11.51        10.39         7.59         2.86         1.22 
TCGA-28-2502 TCGA-28-2513 TCGA-28-5209 TCGA-28-5216 TCGA-32-1977 TCGA-32-1982 
        0.66         7.30        14.53        13.64         0.10         4.67 
TCGA-32-1991 TCGA-32-2495 TCGA-32-2634 TCGA-32-4210 TCGA-32-4213 TCGA-32-5222 
       16.93        15.02        22.78         3.72        19.86        19.23 
TCGA-41-2571 TCGA-41-2573 TCGA-41-3915 TCGA-41-4097 TCGA-74-6577 TCGA-76-4925 
        0.85         8.94        11.84         0.20         4.34         4.80 
TCGA-76-4927 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
       17.59         9.17         2.53        10.78        16.70         3.29 
TCGA-76-6286 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6664 TCGA-81-5910 
       20.98         5.03         0.23         9.27         7.79         1.61 
TCGA-81-5911 
       17.72 

$`PTEN WILD-TYPE`
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        4.73         2.83        14.73        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
        2.70         6.15         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-06-0158 TCGA-06-0165 
        2.33        46.59        12.33        13.94        10.82        10.65 
TCGA-06-0167 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0185 
       11.41         3.29         4.47         3.22        88.14        73.84 
TCGA-06-0189 TCGA-06-0209 TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
       15.42         7.63        15.02         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
       20.42        48.69         5.75         5.75         9.80        23.57 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0877 
       14.20        46.88         7.86         2.70         0.92         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-1806 TCGA-06-2557 TCGA-06-2562 TCGA-06-2563 
        7.17        40.41        15.32         1.08        12.56        30.64 
TCGA-06-2564 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        5.95         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5856 TCGA-06-5859 
        8.81         8.98         8.55         5.10         3.75         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
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-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       18.02        15.35        14.73        34.92        26.66         3.65 
TCGA-12-0821 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.62        10.95        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0740 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        2.04        11.97        23.05         2.24        11.24        13.78 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1450 TCGA-14-1456 
        5.39         2.89        28.93         0.79        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-15-0742 TCGA-15-1444 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
       13.78        50.53        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        7.53         0.16        24.23         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5954 TCGA-19-5958 TCGA-19-5960 TCGA-26-1439 
       17.19         8.02        12.10        14.07        14.96        13.87 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
       31.33        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 
        7.92         5.06        16.60         9.86        24.23        21.30 
TCGA-27-1836 TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2527 TCGA-27-2528 
       30.05        24.76        10.39        16.08        14.40        15.78 
TCGA-28-1747 TCGA-28-2499 TCGA-28-2509 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        2.53         3.12         4.77         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-32-1970 TCGA-32-1979 TCGA-32-1980 
       22.68        12.76         5.42        15.39        19.50         1.18 
TCGA-32-1986 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 
       12.69        12.23        20.78        15.95         8.84        25.18 
TCGA-32-4208 TCGA-32-4209 TCGA-32-4211 TCGA-32-4719 TCGA-41-2572 TCGA-41-2575 
       21.14        20.32        12.59        10.85        13.35         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        0.99         4.44        15.12        12.46         3.45        20.91 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4932 
       14.33         7.50         4.54         3.09         3.65        47.93 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6663 
        2.70        11.38        17.06         8.35         4.83         7.73 
TCGA-87-5896 
       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 
          9.40          11.24 
[1] "0.1 - 69.9 (9.4)"   "0.2 - 120.6 (11.2)"
[1] "hr=" "1.1"
D4V2, continuous
D4V3, binary
                cls
clus               0   1
  PTEN MUTATED    33  52
  PTEN WILD-TYPE  67 126
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     33   52
  PTEN WILD-TYPE   67  126
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           33             67
  MALE             52            126
[1] 2 2
[1] FALSE
D4V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PTEN MUTATED                               0                   2
  PTEN WILD-TYPE                             9                   2
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  PTEN MUTATED                                83
  PTEN WILD-TYPE                             182
D4V5, multiclass
                                 clus
vv                                PTEN MUTATED PTEN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0              9
  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"
D4V6, binary
                cls
clus               0   1
  PTEN MUTATED    55  30
  PTEN WILD-TYPE 131  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     55   30
  PTEN WILD-TYPE  131   62
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            55            131
  YES           30             62
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       1                         5    78
  PTEN WILD-TYPE     4                        12   172
D4V7, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            5             12
  WHITE                               78            172
[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
  PTEN MUTATED     2  67
  PTEN WILD-TYPE   1 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2   67
  PTEN WILD-TYPE    1  153
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                2              1
  NOT HISPANIC OR LATINO           67            153
[1] 2 2
[1] FALSE

Clustering(5) Variable = NF1 MUTATION ANALYSIS
D5V1, survival
               sevent
clus2             0   1
  NF1 MUTATED     6  23
  NF1 WILD-TYPE  61 188
  NF1 MUTATED NF1 WILD-TYPE 
           29           249 
  NF1 MUTATED NF1 WILD-TYPE 
           23           188 
$`NF1 MUTATED`
TCGA-02-0033 TCGA-06-0119 TCGA-06-0124 TCGA-06-0184 TCGA-06-0192 TCGA-06-0214 
        2.83         2.70        20.38        69.90        38.96        15.02 
TCGA-06-2562 TCGA-06-2569 TCGA-06-5410 TCGA-06-5412 TCGA-06-6698 TCGA-14-0789 
       12.56         0.43         3.55         4.54         4.77        11.24 
TCGA-14-0871 TCGA-14-1043 TCGA-19-2620 TCGA-19-5953 TCGA-26-5133 TCGA-28-2502 
       28.93         0.79         4.87         4.73        14.86         0.66 
TCGA-28-5208 TCGA-28-6450 TCGA-32-1980 TCGA-32-1986 TCGA-32-2494 TCGA-41-3392 
       17.88         5.42         1.18        12.69        20.78         0.99 
TCGA-41-4097 TCGA-41-6646 TCGA-74-6575 TCGA-76-6657 TCGA-76-6663 
        0.20        12.46        20.91         5.03         7.73 

$`NF1 WILD-TYPE`
TCGA-02-0003 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
        4.73        14.73         2.50        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0122 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       20.32         6.15         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-06-0185 TCGA-06-0188 TCGA-06-0189 
        4.47         3.22        88.14        73.84        44.58        15.42 
TCGA-06-0195 TCGA-06-0209 TCGA-06-0213 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.40         7.63         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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
       30.64         5.95        16.64         4.37        31.50        11.74 
TCGA-06-5411 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 
        8.35         8.81         8.98         8.55         5.10         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48       120.56         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        4.77         4.96        18.02        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 
       34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0790 TCGA-14-0813 
       11.97         0.95        23.05         2.24        13.78         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
        5.39         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-15-0742 
        7.63         7.17        17.49         0.39         3.42        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       50.53         3.91         4.31        29.03        25.38         5.06 
TCGA-19-2619 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        9.67         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-19-5954 
        4.50         6.64        17.19         8.02        18.90        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-1442 
        1.78        14.07        16.80        14.96        13.87        31.33 
TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
        9.40         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         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        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        2.53         1.22         3.12         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       14.93        11.28        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-32-1970 
       11.01        13.64         5.16        22.68        12.76        15.39 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 
        0.10        19.50         4.67        16.93        12.23        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-41-3393 TCGA-41-3915 TCGA-41-5651 
       13.35         8.94         9.53         4.44        11.84        15.12 
TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        3.45         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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        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         0.23         9.27         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        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 
         5.42         10.95 
[1] "0.2 - 69.9 (5.4)"   "0.1 - 120.6 (10.9)"
[1] "hr=" "1.2"
D5V2, continuous
D5V3, binary
               cls
clus              0   1
  NF1 MUTATED    11  18
  NF1 WILD-TYPE  89 160
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     11   18
  NF1 WILD-TYPE   89  160
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          11            89
  MALE            18           160
[1] 2 2
[1] FALSE
D5V4, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  NF1 MUTATED                               1                   0
  NF1 WILD-TYPE                             8                   4
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  NF1 MUTATED                                28
  NF1 WILD-TYPE                             237
D5V5, multiclass
                                 clus
vv                                NF1 MUTATED NF1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             1             8
  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"
D5V6, binary
               cls
clus              0   1
  NF1 MUTATED    18  11
  NF1 WILD-TYPE 168  81
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     18   11
  NF1 WILD-TYPE  168   81
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           18           168
  YES          11            81
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED       0                         1    27
  NF1 WILD-TYPE     5                        16   223
D5V7, multiclass
                           clus
vv                          NF1 MUTATED NF1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           1            16
  WHITE                              27           223
[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
  NF1 MUTATED     0  21
  NF1 WILD-TYPE   3 199
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      0   21
  NF1 WILD-TYPE    3  199
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          21           199
[1] 2 2
[1] FALSE

Clustering(6) Variable = IDH1 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED    10   4
  IDH1 WILD-TYPE  57 207
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            264 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4            207 
$`IDH1 MUTATED`
TCGA-02-2483 TCGA-06-0128 TCGA-06-0129 TCGA-06-2570 TCGA-06-5417 TCGA-06-6389 
       15.32        22.72        33.67        31.50         5.10         7.79 
TCGA-06-6701 TCGA-14-1456 TCGA-14-4157 TCGA-15-1444 TCGA-19-2629 TCGA-26-1442 
        4.96        40.96         3.42        50.53        24.23        31.33 
TCGA-27-2521 TCGA-32-4208 
       10.39        21.14 

$`IDH1 WILD-TYPE`
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2485 
        4.73         2.83        14.73         2.50        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0130 
       20.32         2.70         6.15        20.38         6.94        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-06-0209 TCGA-06-0213 TCGA-06-0214 
       15.42        38.96         7.40         7.63         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-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 
       16.57        20.78        26.76        13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 
       16.64         4.37         0.43        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.98         8.55         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        6.15         4.57         5.23         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
       18.02        15.35        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        11.24        13.78         1.35         5.39 
TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1823 
        2.89        28.93         0.79         1.38        58.78        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-15-0742 TCGA-16-0846 
        7.63         7.17        17.49         0.39        13.78         3.91 
TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        4.31        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-26-5133 
       14.07        16.80        14.96        13.87         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
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-27-2523 
       30.05        14.04        11.51        24.76        10.39        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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        3.12         0.66         4.77         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-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-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
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         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         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 
        21.930         10.715 
[1] "3.4 - 50.5 (21.9)"  "0.1 - 120.6 (10.7)"
[1] "hr=" "4.9"
D6V2, continuous
D6V3, binary
                cls
clus               0   1
  IDH1 MUTATED     3  11
  IDH1 WILD-TYPE  97 167
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      3   11
  IDH1 WILD-TYPE   97  167
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE            3             97
  MALE             11            167
[1] 2 2
[1] FALSE
D6V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  IDH1 MUTATED                               1                   0
  IDH1 WILD-TYPE                             8                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  IDH1 MUTATED                                13
  IDH1 WILD-TYPE                             252
D6V5, multiclass
                                 clus
vv                                IDH1 MUTATED IDH1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              1              8
  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"
D6V6, binary
                cls
clus               0   1
  IDH1 MUTATED    13   1
  IDH1 WILD-TYPE 173  91
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     13    1
  IDH1 WILD-TYPE  173   91
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO            13            173
  YES            1             91
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       2                         1    11
  IDH1 WILD-TYPE     3                        16   239
D6V7, multiclass
                           clus
vv                          IDH1 MUTATED IDH1 WILD-TYPE
  ASIAN                                2              3
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                               11            239
[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   3 208
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0   12
  IDH1 WILD-TYPE    3  208
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           12            208
[1] 2 2
[1] FALSE

Clustering(7) Variable = PIK3CA MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED     5  23
  PIK3CA WILD-TYPE  62 188
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              28              250 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              23              188 
$`PIK3CA MUTATED`
TCGA-02-0033 TCGA-02-0047 TCGA-02-2485 TCGA-06-0119 TCGA-06-0166 TCGA-06-0879 
        2.83        14.73        15.45         2.70         5.85        40.41 
TCGA-06-2570 TCGA-06-5413 TCGA-06-5417 TCGA-06-6391 TCGA-12-0821 TCGA-12-5301 
       31.50         8.81         5.10         1.48        10.62         2.04 
TCGA-15-0742 TCGA-19-1790 TCGA-19-5947 TCGA-19-5954 TCGA-26-5136 TCGA-27-1838 
       13.78         5.06         6.64        12.10        18.97        11.51 
TCGA-27-2527 TCGA-28-6450 TCGA-32-2491 TCGA-32-2495 TCGA-41-2572 TCGA-41-5651 
       14.40         5.42        12.23        15.02        13.35        15.12 
TCGA-74-6578 TCGA-76-4928 TCGA-76-6193 TCGA-76-6286 
       14.33         3.09         2.70        20.98 

$`PIK3CA WILD-TYPE`
TCGA-02-0003 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0122 
        4.73         2.50        12.92        15.32        20.32         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-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 
       10.65        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-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40         7.63         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-06-0877 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         5.65         7.17        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 
       11.74         3.55         8.35         4.54         8.98         8.55 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        2.73         3.75         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 
        1.55         4.77         4.96        18.02        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-1597 TCGA-12-3649 
       12.99        34.92        26.66         3.65        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 
        0.95        23.05         2.24        11.24        13.78         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 
        5.39         2.89        28.93         0.79         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-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 
        3.42        50.53         3.91         4.31        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-26-1442 
        1.78        14.07        16.80        14.96        13.87        31.33 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 
        9.40        14.86         5.49         8.88         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         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        10.39        10.39 
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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        3.12         0.66         4.77         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-32-1970 
       11.01        13.64         5.16        22.68        12.76        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-32-2494 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        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-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85         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-74-6584 
        0.20        12.46         3.45        20.91         4.34         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.80         4.54        17.59         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 
        2.53        10.78        16.70         3.29        11.38        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         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.79         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           10.800 
[1] "1.5 - 40.4 (11.8)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.3"
D7V2, continuous
D7V3, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    11  17
  PIK3CA WILD-TYPE  89 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     11   17
  PIK3CA WILD-TYPE   89  161
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             11               89
  MALE               17              161
[1] 2 2
[1] FALSE
D7V4, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PIK3CA MUTATED                               1                   1
  PIK3CA WILD-TYPE                             8                   3
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  PIK3CA MUTATED                                26
  PIK3CA WILD-TYPE                             239
D7V5, multiclass
                                 clus
vv                                PIK3CA MUTATED PIK3CA WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                1                8
  TREATED PRIMARY GBM                          1                3
  UNTREATED PRIMARY (DE NOVO) GBM             26              239
[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"
D7V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    20   8
  PIK3CA WILD-TYPE 166  84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     20    8
  PIK3CA WILD-TYPE  166   84
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              20              166
  YES              8               84
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       0                         3    23
  PIK3CA WILD-TYPE     5                        14   227
D7V7, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              3               14
  WHITE                                 23              227
[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  23
  PIK3CA WILD-TYPE   3 197
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      0   23
  PIK3CA WILD-TYPE    3  197
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             23              197
[1] 2 2
[1] FALSE

Clustering(8) Variable = STAG2 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED     1  11
  STAG2 WILD-TYPE  66 200
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             266 
  STAG2 MUTATED STAG2 WILD-TYPE 
             11             200 
$`STAG2 MUTATED`
TCGA-06-0749 TCGA-06-2561 TCGA-06-6388 TCGA-12-0692 TCGA-12-0821 TCGA-14-0789 
        2.70        17.65         5.23         3.65        10.62        11.24 
TCGA-14-2554 TCGA-19-5955 TCGA-32-5222 TCGA-41-4097 TCGA-74-6577 TCGA-81-5910 
       17.49         1.78        19.23         0.20         4.34         1.61 

$`STAG2 WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.63         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-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        7.86         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 
       15.32         1.08        12.49         4.93        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        5.95        16.64         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6389 
        5.10         2.73         3.75         6.15         4.57         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 
        4.77         1.55         4.77         4.96        18.02        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-1597 TCGA-12-3649 
       14.73        12.99        34.92        26.66        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-14-0787 TCGA-14-0790 TCGA-14-0813 
       11.97         0.95        23.05         2.24        13.78         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 
        5.39         2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 
       13.78        50.53         3.91         4.31        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-19-5958 TCGA-19-5959 TCGA-19-5960 
       18.90         4.73        12.10        14.07        16.80        14.96 
TCGA-26-1439 TCGA-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       13.87        31.33         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
       18.97         1.58         7.92         2.33         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        10.39        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 
        2.86        14.40        15.78         2.53         1.22         3.12 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         4.77         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-32-1970 
       13.64         5.16        22.68        12.76         5.42        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-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       10.85         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        4.44        11.84        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        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        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         0.23         9.27         7.73         7.79 
TCGA-81-5911 TCGA-87-5896 
       17.72        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          10.980 
[1] "0.2 - 19.2 (4.8)"   "0.1 - 120.6 (11.0)"
[1] "hr=" "2.2"
D8V2, continuous
D8V3, binary
                 cls
clus                0   1
  STAG2 MUTATED     5   7
  STAG2 WILD-TYPE  95 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      5    7
  STAG2 WILD-TYPE   95  171
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             5              95
  MALE               7             171
[1] 2 2
[1] FALSE
D8V4, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  STAG2 MUTATED                               0                   0
  STAG2 WILD-TYPE                             9                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  STAG2 MUTATED                                12
  STAG2 WILD-TYPE                             253
D8V5, multiclass
                                 clus
vv                                STAG2 MUTATED STAG2 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0               9
  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"
D8V6, binary
                 cls
clus                0   1
  STAG2 MUTATED     7   5
  STAG2 WILD-TYPE 179  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      7    5
  STAG2 WILD-TYPE  179   87
     clus
vv    STAG2 MUTATED STAG2 WILD-TYPE
  NO              7             179
  YES             5              87
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED       0                         1    10
  STAG2 WILD-TYPE     5                        16   240
D8V7, multiclass
                           clus
vv                          STAG2 MUTATED STAG2 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              16
  WHITE                                10             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"
D8V8, binary
                 cls
clus                0   1
  STAG2 MUTATED     0   8
  STAG2 WILD-TYPE   3 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0    8
  STAG2 WILD-TYPE    3  212
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             212
[1] 2 2
[1] FALSE

Clustering(9) Variable = SEMG2 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  SEMG2 MUTATED     2   9
  SEMG2 WILD-TYPE  65 202
  SEMG2 MUTATED SEMG2 WILD-TYPE 
             11             267 
  SEMG2 MUTATED SEMG2 WILD-TYPE 
              9             202 
$`SEMG2 MUTATED`
TCGA-06-0158 TCGA-06-0185 TCGA-06-0195 TCGA-06-0876 TCGA-06-5856 TCGA-19-2624 
       10.82        73.84         7.40        46.19         3.75         0.16 
TCGA-19-5947 TCGA-27-1833 TCGA-32-1979 TCGA-32-2632 TCGA-41-2575 
        6.64        24.23        19.50         8.84         9.53 

$`SEMG2 WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0214 
       44.58        15.42        38.96         7.63         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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
       20.78        26.76        13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 
        4.54         8.81         8.98         8.55         5.10         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        4.77         4.96        18.02        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 
       34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 
        1.35         5.39         2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 
        0.39         3.42        13.78        50.53         3.91         4.31 
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-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5950 TCGA-19-5951 
        4.08        24.23         7.00         4.50        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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       14.96        13.87        31.33         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        8.88        18.97         1.58         7.92         2.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        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        10.39        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 
        2.86        14.40        15.78         2.53         1.22         3.12 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         4.77         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-32-1970 
       13.64         5.16        22.68        12.76         5.42        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        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  SEMG2 MUTATED SEMG2 WILD-TYPE 
           0.16            0.10 
  SEMG2 MUTATED SEMG2 WILD-TYPE 
          73.84          120.56 
  SEMG2 MUTATED SEMG2 WILD-TYPE 
           9.53           10.95 
[1] "0.2 - 73.8 (9.5)"   "0.1 - 120.6 (10.9)"
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
                 cls
clus                0   1
  SEMG2 MUTATED     4   7
  SEMG2 WILD-TYPE  96 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEMG2 MUTATED      4    7
  SEMG2 WILD-TYPE   96  171
        clus
vv       SEMG2 MUTATED SEMG2 WILD-TYPE
  FEMALE             4              96
  MALE               7             171
[1] 2 2
[1] FALSE
D9V4, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  SEMG2 MUTATED                               0                   0
  SEMG2 WILD-TYPE                             9                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  SEMG2 MUTATED                                11
  SEMG2 WILD-TYPE                             254
D9V5, multiclass
                                 clus
vv                                SEMG2 MUTATED SEMG2 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0               9
  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"
D9V6, binary
                 cls
clus                0   1
  SEMG2 MUTATED     7   4
  SEMG2 WILD-TYPE 179  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEMG2 MUTATED      7    4
  SEMG2 WILD-TYPE  179   88
     clus
vv    SEMG2 MUTATED SEMG2 WILD-TYPE
  NO              7             179
  YES             4              88
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEMG2 MUTATED       0                         2     9
  SEMG2 WILD-TYPE     5                        15   241
D9V7, multiclass
                           clus
vv                          SEMG2 MUTATED SEMG2 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             2              15
  WHITE                                 9             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"
D9V8, binary
                 cls
clus                0   1
  SEMG2 MUTATED     0  11
  SEMG2 WILD-TYPE   3 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEMG2 MUTATED      0   11
  SEMG2 WILD-TYPE    3  209
                        clus
vv                       SEMG2 MUTATED SEMG2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             209
[1] 2 2
[1] FALSE

Clustering(10) Variable = MAP3K1 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  MAP3K1 MUTATED     1   5
  MAP3K1 WILD-TYPE  66 206
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               6              272 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               5              206 
$`MAP3K1 MUTATED`
TCGA-06-0214 TCGA-06-0743 TCGA-06-2559 TCGA-12-0619 TCGA-14-0790 TCGA-26-6173 
       15.02        26.40         4.93        34.92        13.78         7.92 

$`MAP3K1 WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        7.63         0.53        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-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.10        23.57        14.20        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 
       40.41        16.57        20.78        26.76        13.61        15.32 
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-06-5408 TCGA-06-5410 
       16.64         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 
        8.35         4.54         8.81         8.98         8.55         5.10 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        2.73         3.75         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 
        4.77         1.55         4.77         4.96        18.02        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 
       14.73        12.99        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 
        2.04        11.97         0.95        23.05         2.24        11.24 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 
        1.35         5.39         2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 
        0.39         3.42        13.78        50.53         3.91         4.31 
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-26-1442 TCGA-26-5132 
       14.07        16.80        14.96        13.87        31.33         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 
       14.86         5.49         8.88        18.97         1.58         2.33 
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        10.39        10.39 
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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        1.22         3.12         0.66         4.77         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-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        5.42        15.39         0.10        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-32-4209 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-41-5651 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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        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 
            14.4             10.8 
[1] "4.9 - 34.9 (14.4)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.2"
D10V2, continuous
D10V3, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     1   5
  MAP3K1 WILD-TYPE  99 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      1    5
  MAP3K1 WILD-TYPE   99  173
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  FEMALE              1               99
  MALE                5              173
[1] 2 2
[1] FALSE
D10V4, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  MAP3K1 MUTATED                               0                   0
  MAP3K1 WILD-TYPE                             9                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  MAP3K1 MUTATED                                 6
  MAP3K1 WILD-TYPE                             259
D10V5, multiclass
                                 clus
vv                                MAP3K1 MUTATED MAP3K1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                0                9
  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"
D10V6, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     3   3
  MAP3K1 WILD-TYPE 183  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      3    3
  MAP3K1 WILD-TYPE  183   89
     clus
vv    MAP3K1 MUTATED MAP3K1 WILD-TYPE
  NO               3              183
  YES              3               89
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP3K1 MUTATED       0                         0     6
  MAP3K1 WILD-TYPE     5                        17   244
D10V7, multiclass
                           clus
vv                          MAP3K1 MUTATED MAP3K1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0               17
  WHITE                                  6              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"
D10V8, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     0   5
  MAP3K1 WILD-TYPE   3 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      0    5
  MAP3K1 WILD-TYPE    3  215
                        clus
vv                       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5              215
[1] 2 2
[1] FALSE

Clustering(11) Variable = SLC26A3 MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  SLC26A3 MUTATED     2   4
  SLC26A3 WILD-TYPE  65 207
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                6               272 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                4               207 
$`SLC26A3 MUTATED`
TCGA-02-0003 TCGA-06-2563 TCGA-12-0618 TCGA-15-0742 TCGA-28-5216 TCGA-32-4211 
        4.73        30.64        12.99        13.78        13.64        12.59 

$`SLC26A3 WILD-TYPE`
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-06-0209 
       73.84        44.58        15.42        38.96         7.40         7.63 
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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         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-06-5408 
        5.95        16.64         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        5.10         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
       12.85         4.77         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 
       15.35        14.73        34.92        26.66         3.65        10.62 
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-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 
       11.24        13.78         1.35         5.39         2.89        28.93 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 
        0.79         1.38        58.78        40.96        17.85         7.63 
TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-1444 TCGA-16-0846 
        7.17        17.49         0.39         3.42        50.53         3.91 
TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        4.31        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-26-1442 
        1.78        14.07        16.80        14.96        13.87        31.33 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         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 
       10.39        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 TCGA-28-2509 
       15.78         2.53         1.22         3.12         0.66         4.77 
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-28-5218 TCGA-28-5219 
       11.77        31.27        23.44        11.01         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
       12.76         5.42        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-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
        3.72        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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
             4.73              0.10 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
            30.64            120.56 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
           13.315            10.715 
[1] "4.7 - 30.6 (13.3)"  "0.1 - 120.6 (10.7)"
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  SLC26A3 MUTATED     1   5
  SLC26A3 WILD-TYPE  99 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      1    5
  SLC26A3 WILD-TYPE   99  173
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  FEMALE               1                99
  MALE                 5               173
[1] 2 2
[1] FALSE
D11V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  SLC26A3 MUTATED                               0                   0
  SLC26A3 WILD-TYPE                             9                   4
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  SLC26A3 MUTATED                                 6
  SLC26A3 WILD-TYPE                             259
D11V5, multiclass
                                 clus
vv                                SLC26A3 MUTATED SLC26A3 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                 9
  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"
D11V6, binary
                   cls
clus                  0   1
  SLC26A3 MUTATED     6   0
  SLC26A3 WILD-TYPE 180  92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      6    0
  SLC26A3 WILD-TYPE  180   92
     clus
vv    SLC26A3 MUTATED SLC26A3 WILD-TYPE
  NO                6               180
  YES               0                92
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC26A3 MUTATED       0                         0     6
  SLC26A3 WILD-TYPE     5                        17   244
D11V7, multiclass
                           clus
vv                          SLC26A3 MUTATED SLC26A3 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                17
  WHITE                                   6               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
  SLC26A3 MUTATED     0   5
  SLC26A3 WILD-TYPE   3 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      0    5
  SLC26A3 WILD-TYPE    3  215
                        clus
vv                       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               215
[1] 2 2
[1] FALSE

Clustering(12) Variable = ATRX MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  ATRX MUTATED    10   6
  ATRX WILD-TYPE  57 205
  ATRX MUTATED ATRX WILD-TYPE 
            16            262 
  ATRX MUTATED ATRX WILD-TYPE 
             6            205 
$`ATRX MUTATED`
TCGA-02-2483 TCGA-06-0129 TCGA-06-0213 TCGA-06-2570 TCGA-06-5417 TCGA-06-5858 
       15.32        33.67         0.53        31.50         5.10         6.15 
TCGA-06-6388 TCGA-06-6391 TCGA-06-6701 TCGA-14-1456 TCGA-14-4157 TCGA-15-1444 
        5.23         1.48         4.96        40.96         3.42        50.53 
TCGA-19-2629 TCGA-27-2521 TCGA-32-4208 TCGA-74-6575 
       24.23        10.39        21.14        20.91 

$`ATRX WILD-TYPE`
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2485 
        4.73         2.83        14.73         2.50        12.92        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-06-0130 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-06-0209 TCGA-06-0214 
       44.58        15.42        38.96         7.40         7.63        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-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 
       16.57        20.78        26.76        13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 
       16.64         4.37         0.43        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.98         8.55         2.73         3.75 
TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        4.57         7.79         5.39       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-08-0386 TCGA-12-0615 
       12.85         4.77         1.55         4.77        18.02        15.35 
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-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-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 
       11.24        13.78         1.35         5.39         2.89        28.93 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 
        0.79         1.38        58.78        17.85         7.63         7.17 
TCGA-14-2554 TCGA-14-3476 TCGA-15-0742 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 
       17.49         0.39        13.78         3.91         4.31        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-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08         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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       14.96        13.87        31.33         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        8.88        18.97         1.58         7.92         2.33         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-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 
        2.86        14.40        15.78         2.53         1.22         3.12 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         4.77         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-32-1970 
       13.64         5.16        22.68        12.76         5.42        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-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        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-74-6577 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        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        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         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.79         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 
        12.855         10.835 
[1] "0.5 - 50.5 (12.9)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "2.9"
D12V2, continuous
D12V3, binary
                cls
clus               0   1
  ATRX MUTATED     7   9
  ATRX WILD-TYPE  93 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      7    9
  ATRX WILD-TYPE   93  169
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  FEMALE            7             93
  MALE              9            169
[1] 2 2
[1] FALSE
D12V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  ATRX MUTATED                               1                   0
  ATRX WILD-TYPE                             8                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  ATRX MUTATED                                15
  ATRX WILD-TYPE                             250
D12V5, multiclass
                                 clus
vv                                ATRX MUTATED ATRX WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              1              8
  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"
D12V6, binary
                cls
clus               0   1
  ATRX MUTATED    13   3
  ATRX WILD-TYPE 173  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     13    3
  ATRX WILD-TYPE  173   89
     clus
vv    ATRX MUTATED ATRX WILD-TYPE
  NO            13            173
  YES            3             89
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATRX MUTATED       2                         1    12
  ATRX WILD-TYPE     3                        16   238
D12V7, multiclass
                           clus
vv                          ATRX MUTATED ATRX WILD-TYPE
  ASIAN                                2              3
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                               12            238
[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
  ATRX MUTATED     0  13
  ATRX WILD-TYPE   3 207
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      0   13
  ATRX WILD-TYPE    3  207
                        clus
vv                       ATRX MUTATED ATRX WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           13            207
[1] 2 2
[1] FALSE

Clustering(13) Variable = BRAF MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  BRAF MUTATED     1   5
  BRAF WILD-TYPE  66 206
  BRAF MUTATED BRAF WILD-TYPE 
             6            272 
  BRAF MUTATED BRAF WILD-TYPE 
             5            206 
$`BRAF MUTATED`
TCGA-02-0047 TCGA-06-0151 TCGA-06-0185 TCGA-06-0644 TCGA-06-1806 TCGA-76-4928 
       14.73        46.59        73.84        12.62        15.32         3.09 

$`BRAF WILD-TYPE`
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-06-0152 TCGA-06-0154 TCGA-06-0155 
       10.29         2.20         2.33        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-06-0188 
        3.29         4.47         3.22        88.14        69.90        44.58 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0209 TCGA-06-0213 TCGA-06-0214 
       15.42        38.96         7.40         7.63         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-06-0645 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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        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-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        4.77         4.96        18.02        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 
       34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 
        1.35         5.39         2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 
        0.39         3.42        13.78        50.53         3.91         4.31 
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-26-1442 TCGA-26-5132 
       14.07        16.80        14.96        13.87        31.33         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         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        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 
        2.53         1.22         3.12         0.66         4.77         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-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
       12.76         5.42        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-76-4929 
       14.33         7.50         4.80         4.54        17.59         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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        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         10.715 
[1] "3.1 - 73.8 (15.0)"  "0.1 - 120.6 (10.7)"
[1] "hr=" "1.7"
D13V2, continuous
D13V3, binary
                cls
clus               0   1
  BRAF MUTATED     2   4
  BRAF WILD-TYPE  98 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      2    4
  BRAF WILD-TYPE   98  174
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE            2             98
  MALE              4            174
[1] 2 2
[1] FALSE
D13V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  BRAF MUTATED                               2                   0
  BRAF WILD-TYPE                             7                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  BRAF MUTATED                                 4
  BRAF WILD-TYPE                             261
D13V5, multiclass
                                 clus
vv                                BRAF MUTATED BRAF WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              2              7
  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"
D13V6, binary
                cls
clus               0   1
  BRAF MUTATED     3   3
  BRAF WILD-TYPE 183  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      3    3
  BRAF WILD-TYPE  183   89
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO             3            183
  YES            3             89
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED       0                         1     5
  BRAF WILD-TYPE     5                        16   245
D13V7, multiclass
                           clus
vv                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                                5            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"
D13V8, binary
                cls
clus               0   1
  BRAF MUTATED     0   5
  BRAF WILD-TYPE   3 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      0    5
  BRAF WILD-TYPE    3  215
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5            215
[1] 2 2
[1] FALSE

Clustering(14) Variable = EGFR MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  EGFR MUTATED    15  58
  EGFR WILD-TYPE  52 153
  EGFR MUTATED EGFR WILD-TYPE 
            73            205 
  EGFR MUTATED EGFR WILD-TYPE 
            58            153 
$`EGFR MUTATED`
TCGA-02-0003 TCGA-02-2485 TCGA-06-0137 TCGA-06-0142 TCGA-06-0154 TCGA-06-0155 
        4.73        15.45        26.70         2.20        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0174 TCGA-06-0185 TCGA-06-0237 TCGA-06-0649 
        3.19        10.82         3.22        73.84        13.64         2.10 
TCGA-06-0650 TCGA-06-0743 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 
       23.57        26.40         2.70         2.70         0.92        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-1804 TCGA-06-2557 TCGA-06-2561 
        7.17        40.41        16.57        13.61         1.08        17.65 
TCGA-06-2563 TCGA-06-2565 TCGA-06-2567 TCGA-06-5413 TCGA-06-5856 TCGA-06-6695 
       30.64        16.64         4.37         8.81         3.75         8.32 
TCGA-06-6700 TCGA-12-0616 TCGA-12-0619 TCGA-12-3650 TCGA-12-3652 TCGA-14-0786 
        4.77        14.73        34.92        10.95        34.92        23.05 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-1395 TCGA-14-1456 TCGA-14-1823 
       11.24        13.78         1.35         1.38        40.96        17.85 
TCGA-14-1829 TCGA-14-2554 TCGA-15-0742 TCGA-16-1045 TCGA-19-1790 TCGA-19-2620 
        7.17        17.49        13.78        29.03         5.06         4.87 
TCGA-19-2624 TCGA-19-2625 TCGA-26-1439 TCGA-26-5139 TCGA-27-1831 TCGA-27-1838 
        0.16         4.08        13.87         1.58        16.60        11.51 
TCGA-27-2528 TCGA-28-1747 TCGA-28-5207 TCGA-28-5209 TCGA-28-5213 TCGA-32-1970 
       15.78         2.53        11.28        14.53        31.27        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-81-5910 
        9.17        16.70        17.06         4.83         0.23         1.61 
TCGA-81-5911 
       17.72 

$`EGFR WILD-TYPE`
TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 
        2.83        14.73         2.50        12.92        15.32        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-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0145 
       12.95        25.35        11.90         0.20        10.29         2.33 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 
       46.59        12.33        10.65         5.85        11.41        19.66 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0178 TCGA-06-0184 TCGA-06-0188 TCGA-06-0189 
        3.29         4.47        88.14        69.90        44.58        15.42 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
       38.96         7.40         7.63         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 
        0.72        13.32        20.42        48.69        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0875 
        5.75         9.80        14.20        46.88         7.86        43.46 
TCGA-06-0877 TCGA-06-0882 TCGA-06-0939 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
        5.65        20.78        26.76        15.32        12.49         4.93 
TCGA-06-2562 TCGA-06-2564 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
       12.56         5.95         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 
        8.35         4.54         8.98         8.55         5.10         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6701 
      120.56         7.36        12.85         4.77         1.55         4.96 
TCGA-08-0386 TCGA-12-0615 TCGA-12-0618 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 
       18.02        15.35        12.99        26.66         3.65        10.62 
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-14-0787 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 
       11.97         0.95         2.24         5.39         2.89        28.93 
TCGA-14-1043 TCGA-14-1450 TCGA-14-1825 TCGA-14-3476 TCGA-14-4157 TCGA-15-1444 
        0.79        58.78         7.63         0.39         3.42        50.53 
TCGA-16-0846 TCGA-16-0861 TCGA-19-1390 TCGA-19-2619 TCGA-19-2623 TCGA-19-2629 
        3.91         4.31        25.38         9.67         7.53        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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
       31.33         9.40        14.86         5.49         8.88        18.97 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        7.92         2.33         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        10.39        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-28-1753 TCGA-28-2499 
       16.08         7.59         2.86        14.40         1.22         3.12 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 
        0.66         4.77         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-32-1977 TCGA-32-1980 TCGA-32-1986 TCGA-32-2491 
       12.76         5.42         0.10         1.18        12.69        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-41-2575 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-76-4928 TCGA-76-4929 
        4.34        14.33         7.50         4.80         3.09         3.65 
TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
       47.93         2.53        10.78         3.29         2.70        11.38 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        8.35        20.98         5.03         9.27         7.73         7.79 
TCGA-87-5896 
       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 
         11.51          10.39 
[1] "0.2 - 73.8 (11.5)"  "0.1 - 120.6 (10.4)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                cls
clus               0   1
  EGFR MUTATED    22  51
  EGFR WILD-TYPE  78 127
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     22   51
  EGFR WILD-TYPE   78  127
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           22             78
  MALE             51            127
[1] 2 2
[1] FALSE
D14V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  EGFR MUTATED                               1                   0
  EGFR WILD-TYPE                             8                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  EGFR MUTATED                                72
  EGFR WILD-TYPE                             193
D14V5, multiclass
                                 clus
vv                                EGFR MUTATED EGFR WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              1              8
  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"
D14V6, binary
                cls
clus               0   1
  EGFR MUTATED    51  22
  EGFR WILD-TYPE 135  70
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     51   22
  EGFR WILD-TYPE  135   70
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO            51            135
  YES           22             70
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED       1                         7    65
  EGFR WILD-TYPE     4                        10   185
D14V7, multiclass
                           clus
vv                          EGFR MUTATED EGFR WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            7             10
  WHITE                               65            185
[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
  EGFR MUTATED     0  53
  EGFR WILD-TYPE   3 167
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0   53
  EGFR WILD-TYPE    3  167
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           53            167
[1] 2 2
[1] FALSE

Clustering(15) Variable = TMPRSS6 MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  TMPRSS6 MUTATED     3   3
  TMPRSS6 WILD-TYPE  64 208
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                6               272 
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                3               208 
$`TMPRSS6 MUTATED`
TCGA-06-0878 TCGA-06-5415 TCGA-19-2629 TCGA-26-5139 TCGA-27-1832 TCGA-76-4928 
        7.17         8.55        24.23         1.58         9.86         3.09 

$`TMPRSS6 WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.63         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-06-0877 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 
        5.65        40.41        16.57        20.78        26.76        13.61 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        5.10         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
       12.85         4.77         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       15.35        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         1.35         5.39         2.89 
TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
       28.93         0.79         1.38        58.78        40.96        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 
        7.63         7.17        17.49         0.39         3.42        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       50.53         3.91         4.31        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-19-5947 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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
       31.33         9.40        14.86         5.49         8.88        18.97 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 
        7.92         2.33         5.06        16.60        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        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 
        2.53         1.22         3.12         0.66         4.77         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-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
       12.76         5.42        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-76-4929 
       14.33         7.50         4.80         4.54        17.59         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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        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             10.98 
[1] "1.6 - 24.2 (7.9)"   "0.1 - 120.6 (11.0)"
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  TMPRSS6 MUTATED     3   3
  TMPRSS6 WILD-TYPE  97 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS6 MUTATED      3    3
  TMPRSS6 WILD-TYPE   97  175
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  FEMALE               3                97
  MALE                 3               175
[1] 2 2
[1] FALSE
D15V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  TMPRSS6 MUTATED                               0                   0
  TMPRSS6 WILD-TYPE                             9                   4
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  TMPRSS6 MUTATED                                 6
  TMPRSS6 WILD-TYPE                             259
D15V5, multiclass
                                 clus
vv                                TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                 9
  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"
D15V6, binary
                   cls
clus                  0   1
  TMPRSS6 MUTATED     5   1
  TMPRSS6 WILD-TYPE 181  91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS6 MUTATED      5    1
  TMPRSS6 WILD-TYPE  181   91
     clus
vv    TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  NO                5               181
  YES               1                91
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMPRSS6 MUTATED       0                         0     6
  TMPRSS6 WILD-TYPE     5                        17   244
D15V7, multiclass
                           clus
vv                          TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                17
  WHITE                                   6               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"
D15V8, binary
                   cls
clus                  0   1
  TMPRSS6 MUTATED     0   5
  TMPRSS6 WILD-TYPE   3 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS6 MUTATED      0    5
  TMPRSS6 WILD-TYPE    3  215
                        clus
vv                       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               215
[1] 2 2
[1] FALSE

Clustering(16) Variable = SEMA3C MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2                0   1
  SEMA3C MUTATED     3   8
  SEMA3C WILD-TYPE  64 203
  SEMA3C MUTATED SEMA3C WILD-TYPE 
              11              267 
  SEMA3C MUTATED SEMA3C WILD-TYPE 
               8              203 
$`SEMA3C MUTATED`
TCGA-02-0033 TCGA-02-2483 TCGA-06-0145 TCGA-06-0646 TCGA-06-0649 TCGA-06-2557 
        2.83        15.32         2.33         5.75         2.10         1.08 
TCGA-06-2558 TCGA-27-1837 TCGA-28-1753 TCGA-32-2634 TCGA-32-5222 
       12.49        14.04         1.22        22.78        19.23 

$`SEMA3C WILD-TYPE`
TCGA-02-0003 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
        4.73        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-06-0129 
        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-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        2.20        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-06-0209 TCGA-06-0213 TCGA-06-0214 
       15.42        38.96         7.40         7.63         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-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
       12.62         5.75         9.80        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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       26.76        13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
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-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
       18.02        15.35        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        11.24        13.78         1.35         5.39 
TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
        2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 
       13.78        50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       14.96        13.87        31.33         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        8.88        18.97         1.58         7.92         2.33         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-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        10.39        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-2499 TCGA-28-2502 
        2.86        14.40        15.78         2.53         3.12         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         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-32-1970 TCGA-32-1977 
        5.16        22.68        12.76         5.42        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-32-2638 TCGA-32-4208 
       20.78        15.02        15.95         8.84        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-41-5651 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        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  SEMA3C MUTATED SEMA3C WILD-TYPE 
            1.08             0.10 
  SEMA3C MUTATED SEMA3C WILD-TYPE 
           22.78           120.56 
  SEMA3C MUTATED SEMA3C WILD-TYPE 
            5.75            10.85 
[1] "1.1 - 22.8 (5.8)"   "0.1 - 120.6 (10.8)"
[1] "hr=" "1.5"
D16V2, continuous
D16V3, binary
                  cls
clus                 0   1
  SEMA3C MUTATED     3   8
  SEMA3C WILD-TYPE  97 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3C MUTATED      3    8
  SEMA3C WILD-TYPE   97  170
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  FEMALE              3               97
  MALE                8              170
[1] 2 2
[1] FALSE
D16V4, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  SEMA3C MUTATED                               0                   0
  SEMA3C WILD-TYPE                             9                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  SEMA3C MUTATED                                11
  SEMA3C WILD-TYPE                             254
D16V5, multiclass
                                 clus
vv                                SEMA3C MUTATED SEMA3C WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                0                9
  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"
D16V6, binary
                  cls
clus                 0   1
  SEMA3C MUTATED     6   5
  SEMA3C WILD-TYPE 180  87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3C MUTATED      6    5
  SEMA3C WILD-TYPE  180   87
     clus
vv    SEMA3C MUTATED SEMA3C WILD-TYPE
  NO               6              180
  YES              5               87
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEMA3C MUTATED       1                         2     8
  SEMA3C WILD-TYPE     4                        15   242
D16V7, multiclass
                           clus
vv                          SEMA3C MUTATED SEMA3C WILD-TYPE
  ASIAN                                  1                4
  BLACK OR AFRICAN AMERICAN              2               15
  WHITE                                  8              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"
D16V8, binary
                  cls
clus                 0   1
  SEMA3C MUTATED     1   9
  SEMA3C WILD-TYPE   2 211
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3C MUTATED      1    9
  SEMA3C WILD-TYPE    2  211
                        clus
vv                       SEMA3C MUTATED SEMA3C WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO              9              211
[1] 2 2
[1] FALSE

Clustering(17) Variable = RPL5 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  RPL5 MUTATED     2   5
  RPL5 WILD-TYPE  65 206
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            271 
  RPL5 MUTATED RPL5 WILD-TYPE 
             5            206 
$`RPL5 MUTATED`
TCGA-02-0047 TCGA-06-0154 TCGA-06-0216 TCGA-06-5413 TCGA-14-0790 TCGA-19-5947 
       14.73        13.94        24.16         8.81        13.78         6.64 
TCGA-26-6174 
        2.33 

$`RPL5 WILD-TYPE`
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-06-0155 
       10.29         2.20         2.33        46.59        12.33        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-06-0209 TCGA-06-0213 
       44.58        15.42        38.96         7.40         7.63         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-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 
       16.57        20.78        26.76        13.61        15.32         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-06-5408 TCGA-06-5410 
       16.64         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 
        8.35         4.54         8.98         8.55         5.10         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 
        1.55         4.77         4.96        18.02        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 
       12.99        34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 
        2.04        11.97         0.95        23.05         2.24        11.24 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 
        1.35         5.39         2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 
        0.39         3.42        13.78        50.53         3.91         4.31 
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-26-1442 TCGA-26-5132 TCGA-26-5133 
       16.80        14.96        13.87        31.33         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-27-1830 
        5.49         8.88        18.97         1.58         7.92         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        10.39        10.39        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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        3.12         0.66         4.77         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-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-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
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        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 
       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          10.82 
[1] "2.3 - 24.2 (13.8)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
                cls
clus               0   1
  RPL5 MUTATED     4   3
  RPL5 WILD-TYPE  96 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      4    3
  RPL5 WILD-TYPE   96  175
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  FEMALE            4             96
  MALE              3            175
[1] 2 2
[1] FALSE
D17V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  RPL5 MUTATED                               0                   0
  RPL5 WILD-TYPE                             9                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  RPL5 MUTATED                                 7
  RPL5 WILD-TYPE                             258
D17V5, multiclass
                                 clus
vv                                RPL5 MUTATED RPL5 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0              9
  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"
D17V6, binary
                cls
clus               0   1
  RPL5 MUTATED     6   1
  RPL5 WILD-TYPE 180  91
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      6    1
  RPL5 WILD-TYPE  180   91
     clus
vv    RPL5 MUTATED RPL5 WILD-TYPE
  NO             6            180
  YES            1             91
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPL5 MUTATED       0                         1     6
  RPL5 WILD-TYPE     5                        16   244
D17V7, multiclass
                           clus
vv                          RPL5 MUTATED RPL5 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                                6            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"
D17V8, binary
                cls
clus               0   1
  RPL5 MUTATED     0   6
  RPL5 WILD-TYPE   3 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      0    6
  RPL5 WILD-TYPE    3  214
                        clus
vv                       RPL5 MUTATED RPL5 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            6            214
[1] 2 2
[1] FALSE

Clustering(18) Variable = PDGFRA MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  PDGFRA MUTATED     1  11
  PDGFRA WILD-TYPE  66 200
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              12              266 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              11              200 
$`PDGFRA MUTATED`
TCGA-02-0047 TCGA-06-0174 TCGA-06-0213 TCGA-06-0214 TCGA-06-0241 TCGA-06-2559 
       14.73         3.22         0.53        15.02        48.69         4.93 
TCGA-14-0740 TCGA-19-1390 TCGA-19-2631 TCGA-26-5134 TCGA-27-1831 TCGA-76-4927 
       11.97        25.38         7.00         5.49        16.60        17.59 

$`PDGFRA WILD-TYPE`
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-06-0209 TCGA-06-0216 
       44.58        15.42        38.96         7.40         7.63        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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 
       26.76        13.61        15.32         1.08        12.49        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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
        4.96        18.02        15.35        14.73        12.99        34.92 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
       26.66         3.65        10.62        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 
       34.92        14.53        14.93         3.22         2.04         0.95 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        11.24        13.78         1.35         5.39 
TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
        2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1790 
       13.78        50.53         3.91         4.31        29.03         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-19-4068 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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
       31.33         9.40        14.86         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        7.92         2.33         5.06         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        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 
        2.53         1.22         3.12         0.66         4.77         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-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
       12.76         5.42        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-76-4928 TCGA-76-4929 
       14.33         7.50         4.80         4.54         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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         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 
           13.35            10.80 
[1] "0.5 - 48.7 (13.4)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                  cls
clus                 0   1
  PDGFRA MUTATED     4   8
  PDGFRA WILD-TYPE  96 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      4    8
  PDGFRA WILD-TYPE   96  170
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  FEMALE              4               96
  MALE                8              170
[1] 2 2
[1] FALSE
D18V4, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PDGFRA MUTATED                               0                   0
  PDGFRA WILD-TYPE                             9                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  PDGFRA MUTATED                                12
  PDGFRA WILD-TYPE                             253
D18V5, multiclass
                                 clus
vv                                PDGFRA MUTATED PDGFRA WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                0                9
  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"
D18V6, binary
                  cls
clus                 0   1
  PDGFRA MUTATED     5   7
  PDGFRA WILD-TYPE 181  85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      5    7
  PDGFRA WILD-TYPE  181   85
     clus
vv    PDGFRA MUTATED PDGFRA WILD-TYPE
  NO               5              181
  YES              7               85
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDGFRA MUTATED       0                         0    12
  PDGFRA WILD-TYPE     5                        17   238
D18V7, multiclass
                           clus
vv                          PDGFRA MUTATED PDGFRA WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0               17
  WHITE                                 12              238
[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
  PDGFRA MUTATED     0  10
  PDGFRA WILD-TYPE   3 210
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      0   10
  PDGFRA WILD-TYPE    3  210
                        clus
vv                       PDGFRA MUTATED PDGFRA WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             10              210
[1] 2 2
[1] FALSE

Clustering(19) Variable = MMP13 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  MMP13 MUTATED     1   4
  MMP13 WILD-TYPE  66 207
  MMP13 MUTATED MMP13 WILD-TYPE 
              5             273 
  MMP13 MUTATED MMP13 WILD-TYPE 
              4             207 
$`MMP13 MUTATED`
TCGA-06-6699 TCGA-12-0688 TCGA-12-3652 TCGA-27-2527 TCGA-76-4925 
        1.55        26.66        34.92        14.40         4.80 

$`MMP13 WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.63         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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 
        7.36         8.32        12.85         4.77         4.77         4.96 
TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0692 
       18.02        15.35        14.73        12.99        34.92         3.65 
TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3653 TCGA-12-5295 
       10.62        22.19        15.22        10.95        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 
       11.24        13.78         1.35         5.39         2.89        28.93 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 
        0.79         1.38        58.78        40.96        17.85         7.63 
TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         0.39         3.42        13.78        50.53 
TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 
        3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
       31.33         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         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        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 TCGA-28-2509 
       15.78         2.53         1.22         3.12         0.66         4.77 
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-32-1970 TCGA-32-1977 TCGA-32-1979 
       22.68        12.76         5.42        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        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        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           10.82 
[1] "1.6 - 34.9 (14.4)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.2"
D19V2, continuous
D19V3, binary
                 cls
clus                0   1
  MMP13 MUTATED     1   4
  MMP13 WILD-TYPE  99 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      1    4
  MMP13 WILD-TYPE   99  174
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  FEMALE             1              99
  MALE               4             174
[1] 2 2
[1] FALSE
D19V4, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  MMP13 MUTATED                               0                   0
  MMP13 WILD-TYPE                             9                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  MMP13 MUTATED                                 5
  MMP13 WILD-TYPE                             260
D19V5, multiclass
                                 clus
vv                                MMP13 MUTATED MMP13 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0               9
  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"
D19V6, binary
                 cls
clus                0   1
  MMP13 MUTATED     5   0
  MMP13 WILD-TYPE 181  92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      5    0
  MMP13 WILD-TYPE  181   92
     clus
vv    MMP13 MUTATED MMP13 WILD-TYPE
  NO              5             181
  YES             0              92
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP13 MUTATED       0                         0     5
  MMP13 WILD-TYPE     5                        17   245
D19V7, multiclass
                           clus
vv                          MMP13 MUTATED MMP13 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              17
  WHITE                                 5             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"
D19V8, binary
                 cls
clus                0   1
  MMP13 MUTATED     0   5
  MMP13 WILD-TYPE   3 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    5
  MMP13 WILD-TYPE    3  215
                        clus
vv                       MMP13 MUTATED MMP13 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5             215
[1] 2 2
[1] FALSE

Clustering(20) Variable = REN MUTATION ANALYSIS
D20V1, survival
               sevent
clus2             0   1
  REN MUTATED     2   3
  REN WILD-TYPE  65 208
  REN MUTATED REN WILD-TYPE 
            5           273 
  REN MUTATED REN WILD-TYPE 
            3           208 
$`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         9.27 

$`REN WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.63         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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       31.50        11.74         3.55         4.54         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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
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-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
       18.02        15.35        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        11.24        13.78         1.35         5.39 
TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
        2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 
       13.78        50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       14.96        13.87        31.33         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        8.88        18.97         1.58         7.92         2.33         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        10.39        10.39        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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        3.12         0.66         4.77         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-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-32-2615 TCGA-32-2632 TCGA-32-2634 
       16.93        12.23        20.78        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-41-3393 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-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 
       20.91        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        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 
       20.98         4.83         5.03         0.23         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  REN MUTATED REN WILD-TYPE 
         0.99          0.10 
  REN MUTATED REN WILD-TYPE 
        15.02        120.56 
  REN MUTATED REN WILD-TYPE 
         8.35         10.95 
[1] "1.0 - 15.0 (8.3)"   "0.1 - 120.6 (10.9)"
[1] "hr=" "1.6"
D20V2, continuous
D20V3, binary
               cls
clus              0   1
  REN MUTATED     1   4
  REN WILD-TYPE  99 174
[1] "tbl2"
               cls
clus            [,1] [,2]
  REN MUTATED      1    4
  REN WILD-TYPE   99  174
        clus
vv       REN MUTATED REN WILD-TYPE
  FEMALE           1            99
  MALE             4           174
[1] 2 2
[1] FALSE
D20V4, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  REN MUTATED                               0                   1
  REN WILD-TYPE                             9                   3
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  REN MUTATED                                 4
  REN WILD-TYPE                             261
D20V5, multiclass
                                 clus
vv                                REN MUTATED REN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             0             9
  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"
D20V6, binary
               cls
clus              0   1
  REN MUTATED     4   1
  REN WILD-TYPE 182  91
[1] "tbl2"
               cls
clus            [,1] [,2]
  REN MUTATED      4    1
  REN WILD-TYPE  182   91
     clus
vv    REN MUTATED REN WILD-TYPE
  NO            4           182
  YES           1            91
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  REN MUTATED       0                         0     4
  REN WILD-TYPE     5                        17   246
D20V7, multiclass
                           clus
vv                          REN MUTATED REN WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            17
  WHITE                               4           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"
D20V8, binary
               cls
clus              0   1
  REN MUTATED     0   4
  REN WILD-TYPE   3 216
[1] "tbl2"
               cls
clus            [,1] [,2]
  REN MUTATED      0    4
  REN WILD-TYPE    3  216
                        clus
vv                       REN MUTATED REN WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           4           216
[1] 2 2
[1] FALSE

Clustering(21) Variable = DSP MUTATION ANALYSIS
D21V1, survival
               sevent
clus2             0   1
  DSP MUTATED     5   5
  DSP WILD-TYPE  62 206
  DSP MUTATED DSP WILD-TYPE 
           10           268 
  DSP MUTATED DSP WILD-TYPE 
            5           206 
$`DSP MUTATED`
TCGA-06-0214 TCGA-06-2567 TCGA-06-6697 TCGA-19-5951 TCGA-27-2527 TCGA-32-2491 
       15.02         4.37        12.85         8.02        14.40        12.23 
TCGA-41-2573 TCGA-74-6575 TCGA-74-6584 TCGA-87-5896 
        8.94        20.91         7.50        26.30 

$`DSP WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        7.63         0.53        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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       30.64         5.95        16.64         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        5.10         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 
        4.77         1.55         4.77         4.96        18.02        15.35 
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-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-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 
       11.24        13.78         1.35         5.39         2.89        28.93 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 
        0.79         1.38        58.78        40.96        17.85         7.63 
TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         0.39         3.42        13.78        50.53 
TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 
        3.91         4.31        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-19-5952 TCGA-19-5953 TCGA-19-5954 
        4.50         6.64        17.19        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-1442 
        1.78        14.07        16.80        14.96        13.87        31.33 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         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-27-2528 
       10.39        10.39        16.08         7.59         2.86        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 
        2.53         1.22         3.12         0.66         4.77         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-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
       12.76         5.42        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-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-76-4925 TCGA-76-4926 
       12.46         3.45         4.34        14.33         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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        7.73         7.79         1.61        17.72 

  DSP MUTATED DSP WILD-TYPE 
         4.37          0.10 
  DSP MUTATED DSP WILD-TYPE 
        26.30        120.56 
  DSP MUTATED DSP WILD-TYPE 
        12.54         10.80 
[1] "4.4 - 26.3 (12.5)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.5"
D21V2, continuous
D21V3, binary
               cls
clus              0   1
  DSP MUTATED     4   6
  DSP WILD-TYPE  96 172
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED      4    6
  DSP WILD-TYPE   96  172
        clus
vv       DSP MUTATED DSP WILD-TYPE
  FEMALE           4            96
  MALE             6           172
[1] 2 2
[1] FALSE
D21V4, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DSP MUTATED                               0                   0
  DSP WILD-TYPE                             9                   4
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  DSP MUTATED                                10
  DSP WILD-TYPE                             255
D21V5, multiclass
                                 clus
vv                                DSP MUTATED DSP WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             0             9
  TREATED PRIMARY GBM                       0             4
  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"
D21V6, binary
               cls
clus              0   1
  DSP MUTATED     8   2
  DSP WILD-TYPE 178  90
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED      8    2
  DSP WILD-TYPE  178   90
     clus
vv    DSP MUTATED DSP WILD-TYPE
  NO            8           178
  YES           2            90
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DSP MUTATED       0                         0     8
  DSP WILD-TYPE     5                        17   242
D21V7, multiclass
                           clus
vv                          DSP MUTATED DSP WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            17
  WHITE                               8           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"
D21V8, binary
               cls
clus              0   1
  DSP MUTATED     0   8
  DSP WILD-TYPE   3 212
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED      0    8
  DSP WILD-TYPE    3  212
                        clus
vv                       DSP MUTATED DSP WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           8           212
[1] 2 2
[1] FALSE

Clustering(22) Variable = CHD8 MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  CHD8 MUTATED     3   5
  CHD8 WILD-TYPE  64 206
  CHD8 MUTATED CHD8 WILD-TYPE 
             8            270 
  CHD8 MUTATED CHD8 WILD-TYPE 
             5            206 
$`CHD8 MUTATED`
TCGA-06-1804 TCGA-06-2559 TCGA-06-5410 TCGA-06-5413 TCGA-19-5959 TCGA-26-1442 
       13.61         4.93         3.55         8.81        16.80        31.33 
TCGA-26-6174 TCGA-32-1982 
        2.33         4.67 

$`CHD8 WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.63         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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         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-06-5408 
        5.95        16.64         4.37         0.43        31.50        11.74 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 
        8.35         4.54         8.98         8.55         5.10         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 
        1.55         4.77         4.96        18.02        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 
       12.99        34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 
        2.04        11.97         0.95        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 
       13.78         1.35         5.39         2.89        28.93         0.79 
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-15-0742 TCGA-15-1444 TCGA-16-0846 
       17.49         0.39         3.42        13.78        50.53         3.91 
TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        4.31        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-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5133 
        1.78        14.07        14.96        13.87         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-27-1830 
        5.49         8.88        18.97         1.58         7.92         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        10.39        10.39        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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        3.12         0.66         4.77         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-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1986 TCGA-32-1991 
       15.39         0.10        19.50         1.18        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-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
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         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         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          10.90 
[1] "2.3 - 31.3 (6.9)"   "0.1 - 120.6 (10.9)"
[1] "hr=" "1"  
D22V2, continuous
D22V3, binary
                cls
clus               0   1
  CHD8 MUTATED     5   3
  CHD8 WILD-TYPE  95 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED      5    3
  CHD8 WILD-TYPE   95  175
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  FEMALE            5             95
  MALE              3            175
[1] 2 2
[1] FALSE
D22V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  CHD8 MUTATED                               0                   0
  CHD8 WILD-TYPE                             9                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  CHD8 MUTATED                                 8
  CHD8 WILD-TYPE                             257
D22V5, multiclass
                                 clus
vv                                CHD8 MUTATED CHD8 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0              9
  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"
D22V6, binary
                cls
clus               0   1
  CHD8 MUTATED     4   4
  CHD8 WILD-TYPE 182  88
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED      4    4
  CHD8 WILD-TYPE  182   88
     clus
vv    CHD8 MUTATED CHD8 WILD-TYPE
  NO             4            182
  YES            4             88
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHD8 MUTATED       0                         0     8
  CHD8 WILD-TYPE     5                        17   242
D22V7, multiclass
                           clus
vv                          CHD8 MUTATED CHD8 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             17
  WHITE                                8            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"
D22V8, binary
                cls
clus               0   1
  CHD8 MUTATED     0   8
  CHD8 WILD-TYPE   3 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED      0    8
  CHD8 WILD-TYPE    3  212
                        clus
vv                       CHD8 MUTATED CHD8 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            8            212
[1] 2 2
[1] FALSE

Clustering(23) Variable = KDR MUTATION ANALYSIS
D23V1, survival
               sevent
clus2             0   1
  KDR MUTATED     0   8
  KDR WILD-TYPE  67 203
  KDR MUTATED KDR WILD-TYPE 
            8           270 
  KDR MUTATED KDR WILD-TYPE 
            8           203 
$`KDR MUTATED`
TCGA-06-0128 TCGA-06-0142 TCGA-06-0188 TCGA-06-0241 TCGA-06-0882 TCGA-12-5301 
       22.72         2.20        44.58        48.69        20.78         2.04 
TCGA-76-6282 TCGA-81-5910 
       17.06         1.61 

$`KDR WILD-TYPE`
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-06-0129 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-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
       10.29         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-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0209 TCGA-06-0213 TCGA-06-0214 
       15.42        38.96         7.40         7.63         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0644 
       24.16         0.72        13.64        13.32        20.42        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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       26.76        13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        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-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        4.77         4.96        18.02        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 
       34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 
        0.95        23.05         2.24        11.24        13.78         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 
        5.39         2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 
        3.42        13.78        50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 
       16.80        14.96        13.87        31.33         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
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        10.39        10.39 
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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        1.22         3.12         0.66         4.77         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-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        5.42        15.39         0.10        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-32-4209 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-41-5651 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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        11.38         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5911 TCGA-87-5896 
        0.23         9.27         7.73         7.79        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         10.80 
[1] "1.6 - 48.7 (18.9)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.2"
D23V2, continuous
D23V3, binary
               cls
clus              0   1
  KDR MUTATED     1   7
  KDR WILD-TYPE  99 171
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      1    7
  KDR WILD-TYPE   99  171
        clus
vv       KDR MUTATED KDR WILD-TYPE
  FEMALE           1            99
  MALE             7           171
[1] 2 2
[1] FALSE
D23V4, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  KDR MUTATED                               1                   0
  KDR WILD-TYPE                             8                   4
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  KDR MUTATED                                 7
  KDR WILD-TYPE                             258
D23V5, multiclass
                                 clus
vv                                KDR MUTATED KDR WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             1             8
  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"
D23V6, binary
               cls
clus              0   1
  KDR MUTATED     5   3
  KDR WILD-TYPE 181  89
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      5    3
  KDR WILD-TYPE  181   89
     clus
vv    KDR MUTATED KDR WILD-TYPE
  NO            5           181
  YES           3            89
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDR MUTATED       0                         0     8
  KDR WILD-TYPE     5                        17   242
D23V7, multiclass
                           clus
vv                          KDR MUTATED KDR WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            17
  WHITE                               8           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"
D23V8, binary
               cls
clus              0   1
  KDR MUTATED     0   7
  KDR WILD-TYPE   3 213
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      0    7
  KDR WILD-TYPE    3  213
                        clus
vv                       KDR MUTATED KDR WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           7           213
[1] 2 2
[1] FALSE

Clustering(24) Variable = ODF4 MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  ODF4 MUTATED     0   3
  ODF4 WILD-TYPE  67 208
  ODF4 MUTATED ODF4 WILD-TYPE 
             3            275 
  ODF4 MUTATED ODF4 WILD-TYPE 
             3            208 
$`ODF4 MUTATED`
TCGA-06-0645 TCGA-06-2559 TCGA-19-5952 
        5.75         4.93        18.90 

$`ODF4 WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.63         0.53        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 
       13.32        20.42        48.69        12.62         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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         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-06-5408 
        5.95        16.64         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        5.10         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
       12.85         4.77         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       15.35        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         1.35         5.39         2.89 
TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
       28.93         0.79         1.38        58.78        40.96        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 
        7.63         7.17        17.49         0.39         3.42        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       50.53         3.91         4.31        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-19-5953 
        7.00         4.50         6.64        17.19         8.02         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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
       31.33         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         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        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 
       14.40        15.78         2.53         1.22         3.12         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         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-32-1970 TCGA-32-1977 
        5.16        22.68        12.76         5.42        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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.73         7.79         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 
          5.75          10.85 
[1] "4.9 - 18.9 (5.8)"   "0.1 - 120.6 (10.8)"
[1] "hr=" "1.7"
D24V2, continuous
D24V3, binary
                cls
clus               0   1
  ODF4 MUTATED     1   2
  ODF4 WILD-TYPE  99 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODF4 MUTATED      1    2
  ODF4 WILD-TYPE   99  176
        clus
vv       ODF4 MUTATED ODF4 WILD-TYPE
  FEMALE            1             99
  MALE              2            176
[1] 2 2
[1] FALSE
D24V4, continuous
[1] "Remove cluster labels:" "ODF4 MUTATED"          
clus
  ODF4 MUTATED ODF4 WILD-TYPE 
             2            198 
    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-06-0184     TCGA-06-0185     TCGA-06-0188 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0192     TCGA-06-0195     TCGA-06-0214     TCGA-06-0216 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0238     TCGA-06-0240     TCGA-06-0241     TCGA-06-0644 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0646     TCGA-06-0648     TCGA-06-0743     TCGA-06-0744 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0745     TCGA-06-0747     TCGA-06-0750     TCGA-06-0875 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0876     TCGA-06-0878     TCGA-06-0879     TCGA-06-0881 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0882     TCGA-06-0939     TCGA-06-1806     TCGA-06-2557 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-2558     TCGA-06-2561     TCGA-06-2562     TCGA-06-2563 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-2564     TCGA-06-2565     TCGA-06-2567     TCGA-06-2569 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-2570     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-06-6389     TCGA-06-6390     TCGA-06-6695 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-6697     TCGA-06-6700     TCGA-08-0386     TCGA-12-0615 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-12-0616     TCGA-12-0618     TCGA-12-0619     TCGA-12-0688 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-12-0692     TCGA-12-0821     TCGA-12-1597     TCGA-12-3649 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-12-3650     TCGA-12-3652     TCGA-12-3653     TCGA-12-5299 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-12-5301     TCGA-14-0740     TCGA-14-0786     TCGA-14-0787 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-14-0789     TCGA-14-0790     TCGA-14-0813     TCGA-14-0817 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-14-0862     TCGA-14-0871     TCGA-14-1043     TCGA-14-1395 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-14-1450     TCGA-14-1456     TCGA-14-1823     TCGA-14-1825 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-14-1829     TCGA-14-2554     TCGA-14-4157     TCGA-15-0742 
"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-26-1442     TCGA-26-5132 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-26-5133     TCGA-26-5134     TCGA-26-5139     TCGA-26-6173 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-26-6174     TCGA-27-1830     TCGA-27-1831     TCGA-27-1832 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-27-1833     TCGA-27-1834     TCGA-27-1835     TCGA-27-1836 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-27-1837     TCGA-27-1838     TCGA-27-2518     TCGA-27-2519 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-27-2521     TCGA-27-2523     TCGA-27-2524     TCGA-27-2526 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-27-2527     TCGA-27-2528     TCGA-28-2502     TCGA-28-2509 
"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-32-1982     TCGA-32-1986     TCGA-32-2615     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-76-6280 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-76-6282     TCGA-76-6285     TCGA-76-6286     TCGA-76-6656 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-76-6657     TCGA-76-6661     TCGA-76-6662     TCGA-76-6663 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-76-6664     TCGA-81-5910 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  ODF4 MUTATED                               0                   0
  ODF4 WILD-TYPE                             9                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  ODF4 MUTATED                                 3
  ODF4 WILD-TYPE                             262
D24V5, multiclass
                                 clus
vv                                ODF4 MUTATED ODF4 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0              9
  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"
D24V6, binary
                cls
clus               0   1
  ODF4 MUTATED     1   2
  ODF4 WILD-TYPE 185  90
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODF4 MUTATED      1    2
  ODF4 WILD-TYPE  185   90
     clus
vv    ODF4 MUTATED ODF4 WILD-TYPE
  NO             1            185
  YES            2             90
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ODF4 MUTATED       0                         0     3
  ODF4 WILD-TYPE     5                        17   247
D24V7, multiclass
                           clus
vv                          ODF4 MUTATED ODF4 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             17
  WHITE                                3            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
  ODF4 MUTATED     0   3
  ODF4 WILD-TYPE   3 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODF4 MUTATED      0    3
  ODF4 WILD-TYPE    3  217
                        clus
vv                       ODF4 MUTATED ODF4 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            217
[1] 2 2
[1] FALSE

Clustering(25) Variable = TP63 MUTATION ANALYSIS
D25V1, survival
                sevent
clus2              0   1
  TP63 MUTATED     3   3
  TP63 WILD-TYPE  64 208
  TP63 MUTATED TP63 WILD-TYPE 
             6            272 
  TP63 MUTATED TP63 WILD-TYPE 
             3            208 
$`TP63 MUTATED`
TCGA-06-0744 TCGA-06-5858 TCGA-19-5960 TCGA-32-1977 TCGA-74-6575 TCGA-81-5910 
       46.88         6.15        14.96         0.10        20.91         1.61 

$`TP63 WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.63         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-06-0745 
        9.80         2.10        23.57        14.20        26.40         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 
        8.55         5.10         2.73         3.75         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
       12.85         4.77         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       15.35        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         1.35         5.39         2.89 
TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
       28.93         0.79         1.38        58.78        40.96        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 
        7.63         7.17        17.49         0.39         3.42        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       50.53         3.91         4.31        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-26-1439 
        4.73        12.10         1.78        14.07        16.80        13.87 
TCGA-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
       31.33         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         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        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 
       14.40        15.78         2.53         1.22         3.12         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         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-32-1970 TCGA-32-1979 
        5.16        22.68        12.76         5.42        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        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        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         0.23         9.27         7.73         7.79 
TCGA-81-5911 TCGA-87-5896 
       17.72        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         10.835 
[1] "0.1 - 46.9 (10.6)"  "0.2 - 120.6 (10.8)"
[1] "hr=" "1.8"
D25V2, continuous
D25V3, binary
                cls
clus               0   1
  TP63 MUTATED     3   3
  TP63 WILD-TYPE  97 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      3    3
  TP63 WILD-TYPE   97  175
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  FEMALE            3             97
  MALE              3            175
[1] 2 2
[1] FALSE
D25V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  TP63 MUTATED                               0                   0
  TP63 WILD-TYPE                             9                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  TP63 MUTATED                                 6
  TP63 WILD-TYPE                             259
D25V5, multiclass
                                 clus
vv                                TP63 MUTATED TP63 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0              9
  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"
D25V6, binary
                cls
clus               0   1
  TP63 MUTATED     4   2
  TP63 WILD-TYPE 182  90
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      4    2
  TP63 WILD-TYPE  182   90
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO             4            182
  YES            2             90
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP63 MUTATED       0                         0     5
  TP63 WILD-TYPE     5                        17   245
D25V7, multiclass
                           clus
vv                          TP63 MUTATED TP63 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             17
  WHITE                                5            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"
D25V8, binary
                cls
clus               0   1
  TP63 MUTATED     1   3
  TP63 WILD-TYPE   2 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      1    3
  TP63 WILD-TYPE    2  217
                        clus
vv                       TP63 MUTATED TP63 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            3            217
[1] 2 2
[1] FALSE

Clustering(26) Variable = PRKCD MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  PRKCD MUTATED     2   1
  PRKCD WILD-TYPE  65 210
  PRKCD MUTATED PRKCD WILD-TYPE 
              3             275 
  PRKCD MUTATED PRKCD WILD-TYPE 
              1             210 
$`PRKCD MUTATED`
TCGA-06-0145 TCGA-14-4157 TCGA-26-5133 
        2.33         3.42        14.86 

$`PRKCD WILD-TYPE`
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-06-0151 TCGA-06-0152 TCGA-06-0154 
        0.20        10.29         2.20        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-06-0209 
       73.84        44.58        15.42        38.96         7.40         7.63 
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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
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-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
       18.02        15.35        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        11.24        13.78         1.35         5.39 
TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
        2.89        28.93         0.79         1.38        58.78        40.96 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-15-0742 
       17.85         7.63         7.17        17.49         0.39        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
       13.87        31.33         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         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        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 
       14.40        15.78         2.53         1.22         3.12         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         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-32-1970 TCGA-32-1977 
        5.16        22.68        12.76         5.42        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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.73         7.79         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 
           3.42           10.85 
[1] "2.3 - 14.9 (3.4)"   "0.1 - 120.6 (10.8)"
[1] "hr=" "1.1"
D26V2, continuous
D26V3, binary
                 cls
clus                0   1
  PRKCD MUTATED     1   2
  PRKCD WILD-TYPE  99 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      1    2
  PRKCD WILD-TYPE   99  176
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  FEMALE             1              99
  MALE               2             176
[1] 2 2
[1] FALSE
D26V4, continuous
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              2             198 
     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-06-0184      TCGA-06-0185      TCGA-06-0188 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0192      TCGA-06-0195      TCGA-06-0214      TCGA-06-0216 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0238      TCGA-06-0240      TCGA-06-0241      TCGA-06-0644 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0646      TCGA-06-0648      TCGA-06-0743      TCGA-06-0744 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0745      TCGA-06-0747      TCGA-06-0750      TCGA-06-0875 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0876      TCGA-06-0878      TCGA-06-0879      TCGA-06-0881 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0882      TCGA-06-0939      TCGA-06-1806      TCGA-06-2557 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5858 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5859      TCGA-06-6388      TCGA-06-6389      TCGA-06-6390 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6695      TCGA-06-6697      TCGA-06-6700      TCGA-08-0386 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-0615      TCGA-12-0616      TCGA-12-0618      TCGA-12-0619 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-0688      TCGA-12-0692      TCGA-12-0821      TCGA-12-1597 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-3649      TCGA-12-3650      TCGA-12-3652      TCGA-12-3653 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-5299      TCGA-12-5301      TCGA-14-0740      TCGA-14-0786 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0787      TCGA-14-0789      TCGA-14-0790      TCGA-14-0813 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0817      TCGA-14-0862      TCGA-14-0871      TCGA-14-1043 
"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-15-0742 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-1390      TCGA-19-1790      TCGA-19-2619      TCGA-19-2620 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-2623      TCGA-19-2631      TCGA-19-4068      TCGA-19-5947 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5950      TCGA-19-5951      TCGA-19-5952      TCGA-19-5954 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5958      TCGA-19-5959      TCGA-19-5960      TCGA-26-1442 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-26-5132      TCGA-26-5134      TCGA-26-5139      TCGA-26-6173 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-26-6174      TCGA-27-1830      TCGA-27-1831      TCGA-27-1832 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1833      TCGA-27-1834      TCGA-27-1835      TCGA-27-1836 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1837      TCGA-27-1838      TCGA-27-2518      TCGA-27-2519 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-2521      TCGA-27-2523      TCGA-27-2524      TCGA-27-2526 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-2527      TCGA-27-2528      TCGA-28-2502      TCGA-28-2509 
"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-32-1982      TCGA-32-1986      TCGA-32-2615      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-76-6280 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6282      TCGA-76-6285      TCGA-76-6286      TCGA-76-6656 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6657      TCGA-76-6661      TCGA-76-6662      TCGA-76-6663 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6664      TCGA-81-5910 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PRKCD MUTATED                               0                   0
  PRKCD WILD-TYPE                             9                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  PRKCD MUTATED                                 3
  PRKCD WILD-TYPE                             262
D26V5, multiclass
                                 clus
vv                                PRKCD MUTATED PRKCD WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0               9
  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"
D26V6, binary
                 cls
clus                0   1
  PRKCD MUTATED     2   1
  PRKCD WILD-TYPE 184  91
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      2    1
  PRKCD WILD-TYPE  184   91
     clus
vv    PRKCD MUTATED PRKCD WILD-TYPE
  NO              2             184
  YES             1              91
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRKCD MUTATED       0                         1     2
  PRKCD WILD-TYPE     5                        16   248
D26V7, multiclass
                           clus
vv                          PRKCD MUTATED PRKCD WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              16
  WHITE                                 2             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"
D26V8, binary
                 cls
clus                0   1
  PRKCD MUTATED     0   2
  PRKCD WILD-TYPE   3 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      0    2
  PRKCD WILD-TYPE    3  218
                        clus
vv                       PRKCD MUTATED PRKCD WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             218
[1] 2 2
[1] FALSE

Clustering(27) Variable = ACSM2B MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  ACSM2B MUTATED     3   1
  ACSM2B WILD-TYPE  64 210
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               4              274 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               1              210 
$`ACSM2B MUTATED`
TCGA-02-2485 TCGA-06-2558 TCGA-27-2519 TCGA-81-5911 
       15.45        12.49        10.39        17.72 

$`ACSM2B WILD-TYPE`
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-02-2486 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-06-0209 
       73.84        44.58        15.42        38.96         7.40         7.63 
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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         1.08         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        5.95        16.64         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        5.10         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
       12.85         4.77         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       15.35        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         1.35         5.39         2.89 
TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
       28.93         0.79         1.38        58.78        40.96        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 
        7.63         7.17        17.49         0.39         3.42        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       13.87        31.33         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
       18.97         1.58         7.92         2.33         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-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 
       14.40        15.78         2.53         1.22         3.12         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         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-32-1970 TCGA-32-1977 
        5.16        22.68        12.76         5.42        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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 
        7.73         7.79         1.61        26.30 

  ACSM2B MUTATED ACSM2B WILD-TYPE 
           10.39             0.10 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
           17.72           120.56 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
           13.97            10.80 
[1] "10.4 - 17.7 (14.0)" "0.1 - 120.6 (10.8)"
[1] "hr=" "3.1"
D27V2, continuous
D27V3, binary
                  cls
clus                 0   1
  ACSM2B MUTATED     1   3
  ACSM2B WILD-TYPE  99 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      1    3
  ACSM2B WILD-TYPE   99  175
        clus
vv       ACSM2B MUTATED ACSM2B WILD-TYPE
  FEMALE              1               99
  MALE                3              175
[1] 2 2
[1] FALSE
D27V4, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  ACSM2B MUTATED                               0                   0
  ACSM2B WILD-TYPE                             9                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  ACSM2B MUTATED                                 4
  ACSM2B WILD-TYPE                             261
D27V5, multiclass
                                 clus
vv                                ACSM2B MUTATED ACSM2B WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                0                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"
D27V6, binary
                  cls
clus                 0   1
  ACSM2B MUTATED     4   0
  ACSM2B WILD-TYPE 182  92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      4    0
  ACSM2B WILD-TYPE  182   92
     clus
vv    ACSM2B MUTATED ACSM2B WILD-TYPE
  NO               4              182
  YES              0               92
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACSM2B MUTATED       0                         1     3
  ACSM2B WILD-TYPE     5                        16   247
D27V7, multiclass
                           clus
vv                          ACSM2B MUTATED ACSM2B WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              1               16
  WHITE                                  3              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"
D27V8, binary
                  cls
clus                 0   1
  ACSM2B MUTATED     0   3
  ACSM2B WILD-TYPE   3 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      0    3
  ACSM2B WILD-TYPE    3  217
                        clus
vv                       ACSM2B MUTATED ACSM2B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              217
[1] 2 2
[1] FALSE

Clustering(28) Variable = CLCN7 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  CLCN7 MUTATED     2   2
  CLCN7 WILD-TYPE  65 209
  CLCN7 MUTATED CLCN7 WILD-TYPE 
              4             274 
  CLCN7 MUTATED CLCN7 WILD-TYPE 
              2             209 
$`CLCN7 MUTATED`
TCGA-06-0169 TCGA-06-0875 TCGA-27-1830 TCGA-28-2502 
        3.29        43.46         5.06         0.66 

$`CLCN7 WILD-TYPE`
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-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 
       11.41        19.66         4.47         3.22        88.14        69.90 
TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0209 
       73.84        44.58        15.42        38.96         7.40         7.63 
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-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         2.70         0.92        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 
       40.41        16.57        20.78        26.76        13.61        15.32 
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-06-5408 
        5.95        16.64         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        5.10         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
       12.85         4.77         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       15.35        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         1.35         5.39         2.89 
TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
       28.93         0.79         1.38        58.78        40.96        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 
        7.63         7.17        17.49         0.39         3.42        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       13.87        31.33         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1831 TCGA-27-1832 
       18.97         1.58         7.92         2.33        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        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2509 
       14.40        15.78         2.53         1.22         3.12         4.77 
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-32-1970 TCGA-32-1977 TCGA-32-1979 
       22.68        12.76         5.42        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        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        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         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.79         1.61        17.72        26.30 

  CLCN7 MUTATED CLCN7 WILD-TYPE 
           0.66            0.10 
  CLCN7 MUTATED CLCN7 WILD-TYPE 
          43.46          120.56 
  CLCN7 MUTATED CLCN7 WILD-TYPE 
          4.175          10.900 
[1] "0.7 - 43.5 (4.2)"   "0.1 - 120.6 (10.9)"
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
                 cls
clus                0   1
  CLCN7 MUTATED     1   3
  CLCN7 WILD-TYPE  99 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN7 MUTATED      1    3
  CLCN7 WILD-TYPE   99  175
        clus
vv       CLCN7 MUTATED CLCN7 WILD-TYPE
  FEMALE             1              99
  MALE               3             175
[1] 2 2
[1] FALSE
D28V4, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  CLCN7 MUTATED                               0                   0
  CLCN7 WILD-TYPE                             9                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  CLCN7 MUTATED                                 4
  CLCN7 WILD-TYPE                             261
D28V5, multiclass
                                 clus
vv                                CLCN7 MUTATED CLCN7 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0               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"
D28V6, binary
                 cls
clus                0   1
  CLCN7 MUTATED     4   0
  CLCN7 WILD-TYPE 182  92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN7 MUTATED      4    0
  CLCN7 WILD-TYPE  182   92
     clus
vv    CLCN7 MUTATED CLCN7 WILD-TYPE
  NO              4             182
  YES             0              92
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLCN7 MUTATED       0                         0     4
  CLCN7 WILD-TYPE     5                        17   246
D28V7, multiclass
                           clus
vv                          CLCN7 MUTATED CLCN7 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              17
  WHITE                                 4             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"
D28V8, binary
                 cls
clus                0   1
  CLCN7 MUTATED     0   4
  CLCN7 WILD-TYPE   3 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN7 MUTATED      0    4
  CLCN7 WILD-TYPE    3  216
                        clus
vv                       CLCN7 MUTATED CLCN7 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             216
[1] 2 2
[1] FALSE

Clustering(29) Variable = DDX5 MUTATION ANALYSIS
D29V1, survival
                sevent
clus2              0   1
  DDX5 MUTATED     0   3
  DDX5 WILD-TYPE  67 208
  DDX5 MUTATED DDX5 WILD-TYPE 
             3            275 
  DDX5 MUTATED DDX5 WILD-TYPE 
             3            208 
$`DDX5 MUTATED`
TCGA-06-0142 TCGA-32-1986 TCGA-76-4925 
        2.20        12.69         4.80 

$`DDX5 WILD-TYPE`
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-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        0.20        10.29         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-06-0209 
       73.84        44.58        15.42        38.96         7.40         7.63 
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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
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-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
       18.02        15.35        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        11.24        13.78         1.35         5.39 
TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
        2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 
       13.78        50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       14.96        13.87        31.33         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        8.88        18.97         1.58         7.92         2.33         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        10.39        10.39        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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        3.12         0.66         4.77         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-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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.73         7.79         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 
          4.80          10.85 
[1] "2.2 - 12.7 (4.8)"   "0.1 - 120.6 (10.8)"
[1] "hr=" "3.2"
D29V2, continuous
D29V3, binary
                cls
clus               0   1
  DDX5 MUTATED     0   3
  DDX5 WILD-TYPE 100 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      0    3
  DDX5 WILD-TYPE  100  175
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  FEMALE            0            100
  MALE              3            175
[1] 2 2
[1] FALSE
D29V4, continuous
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             2            198 
    TCGA-02-0003     TCGA-02-0033     TCGA-02-0047     TCGA-02-0055 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-02-2470     TCGA-02-2483     TCGA-02-2485     TCGA-02-2486 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0126     TCGA-06-0128     TCGA-06-0129     TCGA-06-0130 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0139     TCGA-06-0140     TCGA-06-0141     TCGA-06-0151 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0154     TCGA-06-0155     TCGA-06-0157     TCGA-06-0158 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0165     TCGA-06-0167     TCGA-06-0168     TCGA-06-0169 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0184     TCGA-06-0185     TCGA-06-0188 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0192     TCGA-06-0195     TCGA-06-0214     TCGA-06-0216 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0238     TCGA-06-0240     TCGA-06-0241     TCGA-06-0644 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0646     TCGA-06-0648     TCGA-06-0743     TCGA-06-0744 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0745     TCGA-06-0747     TCGA-06-0750     TCGA-06-0875 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0876     TCGA-06-0878     TCGA-06-0879     TCGA-06-0881 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0882     TCGA-06-0939     TCGA-06-1806     TCGA-06-2557 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2558     TCGA-06-2559     TCGA-06-2561     TCGA-06-2562 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2563     TCGA-06-2564     TCGA-06-2565     TCGA-06-2567 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2569     TCGA-06-2570     TCGA-06-5408     TCGA-06-5410 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5411     TCGA-06-5412     TCGA-06-5413     TCGA-06-5414 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5415     TCGA-06-5417     TCGA-06-5418     TCGA-06-5858 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5859     TCGA-06-6388     TCGA-06-6389     TCGA-06-6390 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6695     TCGA-06-6697     TCGA-06-6700     TCGA-08-0386 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-0615     TCGA-12-0616     TCGA-12-0618     TCGA-12-0619 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-0688     TCGA-12-0692     TCGA-12-0821     TCGA-12-1597 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-3649     TCGA-12-3650     TCGA-12-3652     TCGA-12-3653 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-5299     TCGA-12-5301     TCGA-14-0740     TCGA-14-0786 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-0787     TCGA-14-0789     TCGA-14-0790     TCGA-14-0813 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-0817     TCGA-14-0862     TCGA-14-0871     TCGA-14-1043 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-1395     TCGA-14-1450     TCGA-14-1456     TCGA-14-1823 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-1825     TCGA-14-1829     TCGA-14-2554     TCGA-14-4157 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-15-0742     TCGA-19-1390     TCGA-19-1790     TCGA-19-2619 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-2620     TCGA-19-2623     TCGA-19-2631     TCGA-19-4068 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5947     TCGA-19-5950     TCGA-19-5951     TCGA-19-5952 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5954     TCGA-19-5958     TCGA-19-5959     TCGA-19-5960 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-26-1442     TCGA-26-5132     TCGA-26-5133     TCGA-26-5134 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-26-5139     TCGA-26-6173     TCGA-26-6174     TCGA-27-1830 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1831     TCGA-27-1832     TCGA-27-1833     TCGA-27-1834 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1835     TCGA-27-1836     TCGA-27-1837     TCGA-27-1838 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-2518     TCGA-27-2519     TCGA-27-2521     TCGA-27-2523 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-2524     TCGA-27-2526     TCGA-27-2527     TCGA-27-2528 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-2502     TCGA-28-2509     TCGA-28-2513     TCGA-28-2514 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5204     TCGA-28-5207     TCGA-28-5208     TCGA-28-5211 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5213     TCGA-28-5214     TCGA-28-5215     TCGA-28-5216 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5219     TCGA-28-5220     TCGA-32-1982     TCGA-32-2615 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-41-2571     TCGA-41-2573     TCGA-41-2575     TCGA-74-6573 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-74-6575     TCGA-74-6577     TCGA-74-6578     TCGA-74-6584 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4926     TCGA-76-4927     TCGA-76-4928     TCGA-76-4929 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4931     TCGA-76-4932     TCGA-76-4934     TCGA-76-4935 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6191     TCGA-76-6192     TCGA-76-6193     TCGA-76-6280 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6282     TCGA-76-6285     TCGA-76-6286     TCGA-76-6656 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6657     TCGA-76-6661     TCGA-76-6662     TCGA-76-6663 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6664     TCGA-81-5910 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DDX5 MUTATED                               1                   0
  DDX5 WILD-TYPE                             8                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  DDX5 MUTATED                                 2
  DDX5 WILD-TYPE                             263
D29V5, multiclass
                                 clus
vv                                DDX5 MUTATED DDX5 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              1              8
  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"
D29V6, binary
                cls
clus               0   1
  DDX5 MUTATED     2   1
  DDX5 WILD-TYPE 184  91
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      2    1
  DDX5 WILD-TYPE  184   91
     clus
vv    DDX5 MUTATED DDX5 WILD-TYPE
  NO             2            184
  YES            1             91
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX5 MUTATED       0                         0     3
  DDX5 WILD-TYPE     5                        17   247
D29V7, multiclass
                           clus
vv                          DDX5 MUTATED DDX5 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             17
  WHITE                                3            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"
D29V8, binary
                cls
clus               0   1
  DDX5 MUTATED     0   3
  DDX5 WILD-TYPE   3 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      0    3
  DDX5 WILD-TYPE    3  217
                        clus
vv                       DDX5 MUTATED DDX5 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            217
[1] 2 2
[1] FALSE

Clustering(30) Variable = FBN3 MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  FBN3 MUTATED     4   7
  FBN3 WILD-TYPE  63 204
  FBN3 MUTATED FBN3 WILD-TYPE 
            11            267 
  FBN3 MUTATED FBN3 WILD-TYPE 
             7            204 
$`FBN3 MUTATED`
TCGA-06-0174 TCGA-06-2564 TCGA-06-6699 TCGA-19-2619 TCGA-27-1838 TCGA-28-2513 
        3.22         5.95         1.55         9.67        11.51         7.30 
TCGA-28-5220 TCGA-32-2495 TCGA-32-4210 TCGA-76-6657 TCGA-81-5910 
       12.76        15.02         3.72         5.03         1.61 

$`FBN3 WILD-TYPE`
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-06-0178 TCGA-06-0184 
       11.41        19.66         3.29         4.47        88.14        69.90 
TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0209 
       73.84        44.58        15.42        38.96         7.40         7.63 
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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       30.64        16.64         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        5.10         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 
       12.85         4.77         4.77         4.96        18.02        15.35 
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-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-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 
       11.24        13.78         1.35         5.39         2.89        28.93 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 
        0.79         1.38        58.78        40.96        17.85         7.63 
TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         0.39         3.42        13.78        50.53 
TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2620 
        3.91         4.31        29.03        25.38         5.06         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-26-1442 
        1.78        14.07        16.80        14.96        13.87        31.33 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 
       40.54        21.30        30.05        14.04        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2514 
        2.53         1.22         3.12         0.66         4.77         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-28-6450 
       23.44        11.01        13.64         5.16        22.68         5.42 
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-32-2615 TCGA-32-2632 TCGA-32-2634 
       16.93        12.23        20.78        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14        20.32        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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        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         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5911 TCGA-87-5896 
        7.79        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          11.01 
[1] "1.6 - 15.0 (6.0)"   "0.1 - 120.6 (11.0)"
[1] "hr=" "1.9"
D30V2, continuous
D30V3, binary
                cls
clus               0   1
  FBN3 MUTATED     5   6
  FBN3 WILD-TYPE  95 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED      5    6
  FBN3 WILD-TYPE   95  172
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  FEMALE            5             95
  MALE              6            172
[1] 2 2
[1] FALSE
D30V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  FBN3 MUTATED                               0                   1
  FBN3 WILD-TYPE                             9                   3
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  FBN3 MUTATED                                10
  FBN3 WILD-TYPE                             255
D30V5, multiclass
                                 clus
vv                                FBN3 MUTATED FBN3 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0              9
  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"
D30V6, binary
                cls
clus               0   1
  FBN3 MUTATED     9   2
  FBN3 WILD-TYPE 177  90
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED      9    2
  FBN3 WILD-TYPE  177   90
     clus
vv    FBN3 MUTATED FBN3 WILD-TYPE
  NO             9            177
  YES            2             90
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBN3 MUTATED       0                         1    10
  FBN3 WILD-TYPE     5                        16   240
D30V7, multiclass
                           clus
vv                          FBN3 MUTATED FBN3 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                               10            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"
D30V8, binary
                cls
clus               0   1
  FBN3 MUTATED     0   9
  FBN3 WILD-TYPE   3 211
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED      0    9
  FBN3 WILD-TYPE    3  211
                        clus
vv                       FBN3 MUTATED FBN3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            9            211
[1] 2 2
[1] FALSE

Clustering(31) Variable = CD1D MUTATION ANALYSIS
D31V1, survival
                sevent
clus2              0   1
  CD1D MUTATED     1   3
  CD1D WILD-TYPE  66 208
  CD1D MUTATED CD1D WILD-TYPE 
             4            274 
  CD1D MUTATED CD1D WILD-TYPE 
             3            208 
$`CD1D MUTATED`
TCGA-06-0184 TCGA-06-6697 TCGA-19-5959 TCGA-76-6285 
       69.90        12.85        16.80         8.35 

$`CD1D WILD-TYPE`
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-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0209 
       73.84        44.58        15.42        38.96         7.40         7.63 
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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
        8.32         4.77         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       15.35        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         1.35         5.39         2.89 
TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
       28.93         0.79         1.38        58.78        40.96        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 
        7.63         7.17        17.49         0.39         3.42        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       50.53         3.91         4.31        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-19-5960 TCGA-26-1439 
        4.73        12.10         1.78        14.07        14.96        13.87 
TCGA-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
       31.33         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         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        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 
       14.40        15.78         2.53         1.22         3.12         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         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-32-1970 TCGA-32-1977 
        5.16        22.68        12.76         5.42        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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.79         1.61        17.72        26.30 

  CD1D MUTATED CD1D WILD-TYPE 
          8.35           0.10 
  CD1D MUTATED CD1D WILD-TYPE 
         69.90         120.56 
  CD1D MUTATED CD1D WILD-TYPE 
        14.825         10.800 
[1] "8.3 - 69.9 (14.8)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.8"
D31V2, continuous
D31V3, binary
                cls
clus               0   1
  CD1D MUTATED     2   2
  CD1D WILD-TYPE  98 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1D MUTATED      2    2
  CD1D WILD-TYPE   98  176
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  FEMALE            2             98
  MALE              2            176
[1] 2 2
[1] FALSE
D31V4, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  CD1D MUTATED                               0                   0
  CD1D WILD-TYPE                             9                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  CD1D MUTATED                                 4
  CD1D WILD-TYPE                             261
D31V5, multiclass
                                 clus
vv                                CD1D MUTATED CD1D WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0              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"
D31V6, binary
                cls
clus               0   1
  CD1D MUTATED     3   1
  CD1D WILD-TYPE 183  91
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1D MUTATED      3    1
  CD1D WILD-TYPE  183   91
     clus
vv    CD1D MUTATED CD1D WILD-TYPE
  NO             3            183
  YES            1             91
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD1D MUTATED       0                         0     4
  CD1D WILD-TYPE     5                        17   246
D31V7, multiclass
                           clus
vv                          CD1D MUTATED CD1D WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             17
  WHITE                                4            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"
D31V8, binary
                cls
clus               0   1
  CD1D MUTATED     0   3
  CD1D WILD-TYPE   3 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1D MUTATED      0    3
  CD1D WILD-TYPE    3  217
                        clus
vv                       CD1D MUTATED CD1D WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            217
[1] 2 2
[1] FALSE

Clustering(32) Variable = TEX15 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  TEX15 MUTATED     3   5
  TEX15 WILD-TYPE  64 206
  TEX15 MUTATED TEX15 WILD-TYPE 
              8             270 
  TEX15 MUTATED TEX15 WILD-TYPE 
              5             206 
$`TEX15 MUTATED`
TCGA-06-0169 TCGA-06-0174 TCGA-06-2557 TCGA-06-5859 TCGA-06-6389 TCGA-19-5959 
        3.29         3.22         1.08         4.57         7.79        16.80 
TCGA-27-1830 TCGA-27-2519 
        5.06        10.39 

$`TEX15 WILD-TYPE`
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-06-0173 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 
       11.41        19.66         4.47        88.14        69.90        73.84 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0209 TCGA-06-0213 
       44.58        15.42        38.96         7.40         7.63         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-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 
       40.41        16.57        20.78        26.76        13.61        15.32 
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-06-5408 TCGA-06-5410 
       16.64         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 
        8.35         4.54         8.81         8.98         8.55         5.10 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 
        2.73         3.75         6.15         5.23         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        4.77         4.96        18.02        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 
       34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 
        1.35         5.39         2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 
        0.39         3.42        13.78        50.53         3.91         4.31 
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-26-1442 TCGA-26-5132 TCGA-26-5133 
       14.07        14.96        13.87        31.33         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
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-27-2521 TCGA-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 
        2.86        14.40        15.78         2.53         1.22         3.12 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         4.77         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-32-1970 
       13.64         5.16        22.68        12.76         5.42        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-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
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         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 

  TEX15 MUTATED TEX15 WILD-TYPE 
           1.08            0.10 
  TEX15 MUTATED TEX15 WILD-TYPE 
          16.80          120.56 
  TEX15 MUTATED TEX15 WILD-TYPE 
          4.815          11.125 
[1] "1.1 - 16.8 (4.8)"   "0.1 - 120.6 (11.1)"
[1] "hr=" "1.9"
D32V2, continuous
D32V3, binary
                 cls
clus                0   1
  TEX15 MUTATED     2   6
  TEX15 WILD-TYPE  98 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED      2    6
  TEX15 WILD-TYPE   98  172
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  FEMALE             2              98
  MALE               6             172
[1] 2 2
[1] FALSE
D32V4, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  TEX15 MUTATED                               0                   0
  TEX15 WILD-TYPE                             9                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  TEX15 MUTATED                                 8
  TEX15 WILD-TYPE                             257
D32V5, multiclass
                                 clus
vv                                TEX15 MUTATED TEX15 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0               9
  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"
D32V6, binary
                 cls
clus                0   1
  TEX15 MUTATED     7   1
  TEX15 WILD-TYPE 179  91
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED      7    1
  TEX15 WILD-TYPE  179   91
     clus
vv    TEX15 MUTATED TEX15 WILD-TYPE
  NO              7             179
  YES             1              91
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TEX15 MUTATED       0                         1     7
  TEX15 WILD-TYPE     5                        16   243
D32V7, multiclass
                           clus
vv                          TEX15 MUTATED TEX15 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              16
  WHITE                                 7             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"
D32V8, binary
                 cls
clus                0   1
  TEX15 MUTATED     0   8
  TEX15 WILD-TYPE   3 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED      0    8
  TEX15 WILD-TYPE    3  212
                        clus
vv                       TEX15 MUTATED TEX15 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             212
[1] 2 2
[1] FALSE

Clustering(33) Variable = KEL MUTATION ANALYSIS
D33V1, survival
               sevent
clus2             0   1
  KEL MUTATED     3  12
  KEL WILD-TYPE  64 199
  KEL MUTATED KEL WILD-TYPE 
           15           263 
  KEL MUTATED KEL WILD-TYPE 
           12           199 
$`KEL MUTATED`
TCGA-06-0145 TCGA-06-0152 TCGA-06-0192 TCGA-06-0238 TCGA-06-0879 TCGA-06-2558 
        2.33        12.33        38.96        13.32        40.41        12.49 
TCGA-06-2563 TCGA-06-5408 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-12-5301 
       30.64        11.74         4.54         8.98         8.55         2.04 
TCGA-26-5135 TCGA-41-2572 TCGA-76-4929 
        8.88        13.35         3.65 

$`KEL WILD-TYPE`
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-06-0151 TCGA-06-0154 TCGA-06-0155 
        0.20        10.29         2.20        46.59        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-06-0195 TCGA-06-0209 TCGA-06-0213 TCGA-06-0214 
       44.58        15.42         7.40         7.63         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 
       24.16         0.72        13.64        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-06-0877 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         5.65         7.17        16.57        20.78 
TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 
       26.76        13.61        15.32         1.08         4.93        17.65 
TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
       12.56         5.95        16.64         4.37         0.43        31.50 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        3.55         8.35         8.81         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        4.77         4.96        18.02        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 
       34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 
        0.95        23.05         2.24        11.24        13.78         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 
        5.39         2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 
        3.42        13.78        50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 
       16.80        14.96        13.87        31.33         9.40        14.86 
TCGA-26-5134 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        5.49        18.97         1.58         7.92         2.33         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        10.39        10.39        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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        3.12         0.66         4.77         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-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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.73         7.79         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         10.82 
[1] "2.0 - 40.4 (11.7)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
               cls
clus              0   1
  KEL MUTATED     7   8
  KEL WILD-TYPE  93 170
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      7    8
  KEL WILD-TYPE   93  170
        clus
vv       KEL MUTATED KEL WILD-TYPE
  FEMALE           7            93
  MALE             8           170
[1] 2 2
[1] FALSE
D33V4, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  KEL MUTATED                               0                   0
  KEL WILD-TYPE                             9                   4
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  KEL MUTATED                                15
  KEL WILD-TYPE                             250
D33V5, multiclass
                                 clus
vv                                KEL MUTATED KEL WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             0             9
  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"
D33V6, binary
               cls
clus              0   1
  KEL MUTATED    10   5
  KEL WILD-TYPE 176  87
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED     10    5
  KEL WILD-TYPE  176   87
     clus
vv    KEL MUTATED KEL WILD-TYPE
  NO           10           176
  YES           5            87
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KEL MUTATED       0                         0    15
  KEL WILD-TYPE     5                        17   235
D33V7, multiclass
                           clus
vv                          KEL MUTATED KEL WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            17
  WHITE                              15           235
[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
  KEL MUTATED     0  15
  KEL WILD-TYPE   3 205
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      0   15
  KEL WILD-TYPE    3  205
                        clus
vv                       KEL MUTATED KEL WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          15           205
[1] 2 2
[1] FALSE

Clustering(34) Variable = MUC17 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  MUC17 MUTATED     2  19
  MUC17 WILD-TYPE  65 192
  MUC17 MUTATED MUC17 WILD-TYPE 
             21             257 
  MUC17 MUTATED MUC17 WILD-TYPE 
             19             192 
$`MUC17 MUTATED`
TCGA-02-0003 TCGA-06-0124 TCGA-06-0168 TCGA-06-0645 TCGA-06-0650 TCGA-06-0939 
        4.73        20.38        19.66         5.75        23.57        26.76 
TCGA-06-2557 TCGA-06-5418 TCGA-12-0821 TCGA-14-1823 TCGA-16-0846 TCGA-19-5953 
        1.08         2.73        10.62        17.85         3.91         4.73 
TCGA-19-5954 TCGA-27-2523 TCGA-28-5204 TCGA-28-5216 TCGA-28-5218 TCGA-32-2491 
       12.10        16.08        14.93        13.64         5.16        12.23 
TCGA-32-4213 TCGA-76-6192 TCGA-76-6286 
       19.86         3.29        20.98 

$`MUC17 WILD-TYPE`
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-06-0126 TCGA-06-0128 TCGA-06-0129 
       20.32         2.70         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-06-0169 
        3.19        10.82        10.65         5.85        11.41         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-06-0209 TCGA-06-0213 TCGA-06-0214 
       15.42        38.96         7.40         7.63         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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61        15.32        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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5417 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         5.10         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
       12.85         4.77         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       15.35        14.73        12.99        34.92        26.66         3.65 
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-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 
       11.24        13.78         1.35         5.39         2.89        28.93 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1825 TCGA-14-1829 
        0.79         1.38        58.78        40.96         7.63         7.17 
TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-16-0861 
       17.49         0.39         3.42        13.78        50.53         4.31 
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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       14.96        13.87        31.33         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        8.88        18.97         1.58         7.92         2.33         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        10.39        10.39         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 
        2.86        14.40        15.78         2.53         1.22         3.12 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 
        0.66         4.77         7.30         5.26        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5219 
       14.53        11.77        31.27        23.44        11.01        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
       12.76         5.42        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-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       12.59        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-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
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-76-6193 TCGA-76-6280 
       47.93         2.53        10.78        16.70         2.70        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
       17.06         8.35         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.73         7.79         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 
          12.23           10.78 
[1] "1.1 - 26.8 (12.2)"  "0.1 - 120.6 (10.8)"
[1] "hr=" "1.3"
D34V2, continuous
D34V3, binary
                 cls
clus                0   1
  MUC17 MUTATED     8  13
  MUC17 WILD-TYPE  92 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      8   13
  MUC17 WILD-TYPE   92  165
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  FEMALE             8              92
  MALE              13             165
[1] 2 2
[1] FALSE
D34V4, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  MUC17 MUTATED                               0                   0
  MUC17 WILD-TYPE                             9                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  MUC17 MUTATED                                21
  MUC17 WILD-TYPE                             244
D34V5, multiclass
                                 clus
vv                                MUC17 MUTATED MUC17 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0               9
  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"
D34V6, binary
                 cls
clus                0   1
  MUC17 MUTATED    14   7
  MUC17 WILD-TYPE 172  85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     14    7
  MUC17 WILD-TYPE  172   85
     clus
vv    MUC17 MUTATED MUC17 WILD-TYPE
  NO             14             172
  YES             7              85
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC17 MUTATED       0                         1    20
  MUC17 WILD-TYPE     5                        16   230
D34V7, multiclass
                           clus
vv                          MUC17 MUTATED MUC17 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              16
  WHITE                                20             230
[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  17
  MUC17 WILD-TYPE   3 203
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      0   17
  MUC17 WILD-TYPE    3  203
                        clus
vv                       MUC17 MUTATED MUC17 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            17             203
[1] 2 2
[1] FALSE

Clustering(35) Variable = SLC6A14 MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  SLC6A14 MUTATED     3   2
  SLC6A14 WILD-TYPE  64 209
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                5               273 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                2               209 
$`SLC6A14 MUTATED`
TCGA-06-0119 TCGA-19-4068 TCGA-27-1832 TCGA-32-2634 TCGA-74-6578 
        2.70         4.50         9.86        22.78        14.33 

$`SLC6A14 WILD-TYPE`
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-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 
       15.45        20.32         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-06-0209 
       73.84        44.58        15.42        38.96         7.40         7.63 
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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
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-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
       18.02        15.35        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        11.24        13.78         1.35         5.39 
TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
        2.89        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 
       13.78        50.53         3.91         4.31        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-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       24.23         7.00         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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       13.87        31.33         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
       18.97         1.58         7.92         2.33         5.06        16.60 
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        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 
       14.40        15.78         2.53         1.22         3.12         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         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-32-1970 TCGA-32-1977 
        5.16        22.68        12.76         5.42        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-32-2638 TCGA-32-4208 
       20.78        15.02        15.95         8.84        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-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
        4.34         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        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
              2.7               0.1 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
            22.78            120.56 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
             9.86             10.85 
[1] "2.7 - 22.8 (9.9)"   "0.1 - 120.6 (10.8)"
[1] "hr=" "1.5"
D35V2, continuous
D35V3, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     3   2
  SLC6A14 WILD-TYPE  97 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      3    2
  SLC6A14 WILD-TYPE   97  176
        clus
vv       SLC6A14 MUTATED SLC6A14 WILD-TYPE
  FEMALE               3                97
  MALE                 2               176
[1] 2 2
[1] FALSE
D35V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  SLC6A14 MUTATED                               1                   0
  SLC6A14 WILD-TYPE                             8                   4
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  SLC6A14 MUTATED                                 4
  SLC6A14 WILD-TYPE                             261
D35V5, multiclass
                                 clus
vv                                SLC6A14 MUTATED SLC6A14 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                 8
  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"
D35V6, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     3   2
  SLC6A14 WILD-TYPE 183  90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      3    2
  SLC6A14 WILD-TYPE  183   90
     clus
vv    SLC6A14 MUTATED SLC6A14 WILD-TYPE
  NO                3               183
  YES               2                90
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC6A14 MUTATED       0                         0     4
  SLC6A14 WILD-TYPE     5                        17   246
D35V7, multiclass
                           clus
vv                          SLC6A14 MUTATED SLC6A14 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                17
  WHITE                                   4               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"
D35V8, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     0   4
  SLC6A14 WILD-TYPE   3 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      0    4
  SLC6A14 WILD-TYPE    3  216
                        clus
vv                       SLC6A14 MUTATED SLC6A14 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               216
[1] 2 2
[1] FALSE

Clustering(36) Variable = LRRC55 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2                0   1
  LRRC55 MUTATED     4   2
  LRRC55 WILD-TYPE  63 209
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               6              272 
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               2              209 
$`LRRC55 MUTATED`
TCGA-06-0185 TCGA-06-0214 TCGA-06-0216 TCGA-06-0875 TCGA-06-5414 TCGA-14-1450 
       73.84        15.02        24.16        43.46         8.98        58.78 

$`LRRC55 WILD-TYPE`
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-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0209 
       69.90        44.58        15.42        38.96         7.40         7.63 
TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.53         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-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
       20.78        26.76        13.61        15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        4.77         4.96        18.02        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 
       34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 
        1.35         5.39         2.89        28.93         0.79         1.38 
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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 
        3.42        13.78        50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 
       16.80        14.96        13.87        31.33         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
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        10.39        10.39 
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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        1.22         3.12         0.66         4.77         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-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        5.42        15.39         0.10        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-32-4209 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-41-5651 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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  LRRC55 MUTATED LRRC55 WILD-TYPE 
            8.98             0.10 
  LRRC55 MUTATED LRRC55 WILD-TYPE 
           73.84           120.56 
  LRRC55 MUTATED LRRC55 WILD-TYPE 
          33.810           10.715 
[1] "9.0 - 73.8 (33.8)"  "0.1 - 120.6 (10.7)"
[1] "hr=" "6.3"
D36V2, continuous
D36V3, binary
                  cls
clus                 0   1
  LRRC55 MUTATED     3   3
  LRRC55 WILD-TYPE  97 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC55 MUTATED      3    3
  LRRC55 WILD-TYPE   97  175
        clus
vv       LRRC55 MUTATED LRRC55 WILD-TYPE
  FEMALE              3               97
  MALE                3              175
[1] 2 2
[1] FALSE
D36V4, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  LRRC55 MUTATED                               0                   0
  LRRC55 WILD-TYPE                             9                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  LRRC55 MUTATED                                 6
  LRRC55 WILD-TYPE                             259
D36V5, multiclass
                                 clus
vv                                LRRC55 MUTATED LRRC55 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                0                9
  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"
D36V6, binary
                  cls
clus                 0   1
  LRRC55 MUTATED     5   1
  LRRC55 WILD-TYPE 181  91
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC55 MUTATED      5    1
  LRRC55 WILD-TYPE  181   91
     clus
vv    LRRC55 MUTATED LRRC55 WILD-TYPE
  NO               5              181
  YES              1               91
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRRC55 MUTATED       0                         1     5
  LRRC55 WILD-TYPE     5                        16   245
D36V7, multiclass
                           clus
vv                          LRRC55 MUTATED LRRC55 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              1               16
  WHITE                                  5              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"
D36V8, binary
                  cls
clus                 0   1
  LRRC55 MUTATED     0   5
  LRRC55 WILD-TYPE   3 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC55 MUTATED      0    5
  LRRC55 WILD-TYPE    3  215
                        clus
vv                       LRRC55 MUTATED LRRC55 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5              215
[1] 2 2
[1] FALSE

Clustering(37) Variable = CD209 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  CD209 MUTATED     2   3
  CD209 WILD-TYPE  65 208
  CD209 MUTATED CD209 WILD-TYPE 
              5             273 
  CD209 MUTATED CD209 WILD-TYPE 
              3             208 
$`CD209 MUTATED`
TCGA-06-0650 TCGA-06-6698 TCGA-19-4068 TCGA-41-2571 TCGA-76-4931 
       23.57         4.77         4.50         0.85         9.17 

$`CD209 WILD-TYPE`
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-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.63         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-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.80         2.10        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         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-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         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-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 
        8.32        12.85         1.55         4.77         4.96        18.02 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       15.35        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         1.35         5.39         2.89 
TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
       28.93         0.79         1.38        58.78        40.96        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-15-0742 
        7.63         7.17        17.49         0.39         3.42        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       50.53         3.91         4.31        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-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         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-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
       31.33         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         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        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 
       14.40        15.78         2.53         1.22         3.12         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         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-32-1970 TCGA-32-1977 
        5.16        22.68        12.76         5.42        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        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        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 
           4.77           10.95 
[1] "0.8 - 23.6 (4.8)"   "0.1 - 120.6 (10.9)"
[1] "hr=" "1.3"
D37V2, continuous
D37V3, binary
                 cls
clus                0   1
  CD209 MUTATED     4   1
  CD209 WILD-TYPE  96 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      4    1
  CD209 WILD-TYPE   96  177
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  FEMALE             4              96
  MALE               1             177
[1] 2 2
[1] FALSE
D37V4, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  CD209 MUTATED                               0                   0
  CD209 WILD-TYPE                             9                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  CD209 MUTATED                                 5
  CD209 WILD-TYPE                             260
D37V5, multiclass
                                 clus
vv                                CD209 MUTATED CD209 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0               9
  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"
D37V6, binary
                 cls
clus                0   1
  CD209 MUTATED     3   2
  CD209 WILD-TYPE 183  90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      3    2
  CD209 WILD-TYPE  183   90
     clus
vv    CD209 MUTATED CD209 WILD-TYPE
  NO              3             183
  YES             2              90
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD209 MUTATED       0                         0     5
  CD209 WILD-TYPE     5                        17   245
D37V7, multiclass
                           clus
vv                          CD209 MUTATED CD209 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              17
  WHITE                                 5             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"
D37V8, binary
                 cls
clus                0   1
  CD209 MUTATED     0   4
  CD209 WILD-TYPE   3 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      0    4
  CD209 WILD-TYPE    3  216
                        clus
vv                       CD209 MUTATED CD209 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             216
[1] 2 2
[1] FALSE

Clustering(38) Variable = LZTR1 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2               0   1
  LZTR1 MUTATED     4   7
  LZTR1 WILD-TYPE  63 204
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             11             267 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              7             204 
$`LZTR1 MUTATED`
TCGA-06-0188 TCGA-06-2562 TCGA-06-5413 TCGA-06-5856 TCGA-06-6697 TCGA-14-0862 
       44.58        12.56         8.81         3.75        12.85         2.89 
TCGA-32-1977 TCGA-32-4209 TCGA-32-4210 TCGA-76-6657 TCGA-76-6664 
        0.10        20.32         3.72         5.03         7.79 

$`LZTR1 WILD-TYPE`
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-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0209 
       69.90        73.84        15.42        38.96         7.40         7.63 
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-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
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-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 
       15.32         1.08        12.49         4.93        17.65        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        5.95        16.64         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 
        3.55         8.35         4.54         8.98         8.55         5.10 
TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        2.73         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 
        1.48       120.56         7.36         8.32         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        4.77         4.96        18.02        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 
       34.92        26.66         3.65        10.62        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-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 
        1.35         5.39        28.93         0.79         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-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 
        3.42        13.78        50.53         3.91         4.31        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-26-1442 TCGA-26-5132 TCGA-26-5133 
       16.80        14.96        13.87        31.33         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
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        10.39        10.39 
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-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        1.22         3.12         0.66         4.77         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-32-1970 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        5.42        15.39        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-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        25.18        21.14        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-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        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         0.23         9.27         7.73 
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 
           7.79           10.95 
[1] "0.1 - 44.6 (7.8)"   "0.2 - 120.6 (10.9)"
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
                 cls
clus                0   1
  LZTR1 MUTATED     2   9
  LZTR1 WILD-TYPE  98 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      2    9
  LZTR1 WILD-TYPE   98  169
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  FEMALE             2              98
  MALE               9             169
[1] 2 2
[1] FALSE
D38V4, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  LZTR1 MUTATED                               0                   1
  LZTR1 WILD-TYPE                             9                   3
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  LZTR1 MUTATED                                10
  LZTR1 WILD-TYPE                             255
D38V5, multiclass
                                 clus
vv                                LZTR1 MUTATED LZTR1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0               9
  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"
D38V6, binary
                 cls
clus                0   1
  LZTR1 MUTATED     6   5
  LZTR1 WILD-TYPE 180  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      6    5
  LZTR1 WILD-TYPE  180   87
     clus
vv    LZTR1 MUTATED LZTR1 WILD-TYPE
  NO              6             180
  YES             5              87
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LZTR1 MUTATED       0                         0    11
  LZTR1 WILD-TYPE     5                        17   239
D38V7, multiclass
                           clus
vv                          LZTR1 MUTATED LZTR1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              17
  WHITE                                11             239
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                 cls
clus                0   1
  LZTR1 MUTATED     2   7
  LZTR1 WILD-TYPE   1 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      2    7
  LZTR1 WILD-TYPE    1  213
                        clus
vv                       LZTR1 MUTATED LZTR1 WILD-TYPE
  HISPANIC OR LATINO                 2               1
  NOT HISPANIC OR LATINO             7             213
[1] 2 2
[1] FALSE
