[1] "ofn"        "-oTKIRP-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/KIRP-TP/22507257/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/22574643/transformed.cor.cli.txt"

nPatients in clinical file=291, in cluster file=282, common to both=282
[1] "Reduce the number of clustering variables from 27 to 26."
[1]  26 282
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             16             266 
  SETD2 MUTATED SETD2 WILD-TYPE 
             16             266 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           10           272 
  NF2 MUTATED NF2 WILD-TYPE 
           10           272 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               9              273 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               9              273 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           21           261 
  MET MUTATED MET WILD-TYPE 
           21           261 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             6            276 
  NEFH MUTATED NEFH WILD-TYPE 
             6            276 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             5            277 
  KRAS MUTATED KRAS WILD-TYPE 
             5            277 
[1] "CUL3 MUTATION ANALYSIS"
[1] 3
  CUL3 MUTATED CUL3 WILD-TYPE 
            10            272 
  CUL3 MUTATED CUL3 WILD-TYPE 
            10            272 
[1] "PCF11 MUTATION ANALYSIS"
[1] 3
  PCF11 MUTATED PCF11 WILD-TYPE 
             11             271 
  PCF11 MUTATED PCF11 WILD-TYPE 
             11             271 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               6              276 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               6              276 
[1] "PAM MUTATION ANALYSIS"
[1] 3
  PAM MUTATED PAM WILD-TYPE 
            3           279 
  PAM MUTATED PAM WILD-TYPE 
            3           279 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                6               276 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                6               276 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             10             272 
  KDM6A MUTATED KDM6A WILD-TYPE 
             10             272 
[1] "AR MUTATION ANALYSIS"
[1] 3
  AR MUTATED AR WILD-TYPE 
          13          269 
  AR MUTATED AR WILD-TYPE 
          13          269 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             7            275 
  TP53 MUTATED TP53 WILD-TYPE 
             7            275 
[1] "KRTAP4-5 MUTATION ANALYSIS"
[1] 3
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 5                277 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 5                277 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             4            278 
  BRAF MUTATED BRAF WILD-TYPE 
             4            278 
[1] "KIAA0922 MUTATION ANALYSIS"
[1] 3
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 5                277 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 5                277 
[1] "KRT2 MUTATION ANALYSIS"
[1] 3
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            277 
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            277 
[1] "ALMS1 MUTATION ANALYSIS"
[1] 3
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              8             274 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              8             274 
[1] "GXYLT1 MUTATION ANALYSIS"
[1] 3
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               4              278 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               4              278 
[1] "ATP1B1 MUTATION ANALYSIS"
[1] 3
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
               7              275 
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
               7              275 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             11             271 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             11             271 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            275 
  PTEN MUTATED PTEN WILD-TYPE 
             7            275 
[1] "SAV1 MUTATION ANALYSIS"
[1] 3
  SAV1 MUTATED SAV1 WILD-TYPE 
             6            276 
  SAV1 MUTATED SAV1 WILD-TYPE 
             6            276 
[1] "CALCR MUTATION ANALYSIS"
[1] 3
  CALCR MUTATED CALCR WILD-TYPE 
              3             279 
  CALCR MUTATED CALCR WILD-TYPE 
              3             279 
[1] "IGSF3 MUTATION ANALYSIS"
[1] 3
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              4             278 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              4             278 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 282 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=41,	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:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "201"   "1"    
freq.contrast "1"     "201"  
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 282 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
189  32  57   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  189    32    59 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
189  32  57   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  189    32    59 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
49 22  3 
[1] "table(vv)"
vv
   N0 N1+N2 
   49    25 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
49 22  3 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 49

$Class1_nSamples
[1] 25

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   49    25 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=37, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=34, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = SETD2 MUTATION ANALYSIS
D1V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    12   4
  SETD2 WILD-TYPE 226  37
  SETD2 MUTATED SETD2 WILD-TYPE 
             16             263 
  SETD2 MUTATED SETD2 WILD-TYPE 
              4              37 
$`SETD2 MUTATED`
TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-A4-A5Y1 TCGA-B9-5155 TCGA-B9-A44B TCGA-4A-A93X 
       33.07        12.26        12.99        21.86        11.87        12.82 
TCGA-5P-A9K3 TCGA-A4-8098 TCGA-B1-A656 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5890 
       15.48        29.46        20.32        86.76         8.88         7.66 
TCGA-BQ-5891 TCGA-BQ-7061 TCGA-GL-A9DE TCGA-SX-A7SM 
        0.95         7.17        16.31        11.93 

$`SETD2 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV 
       34.85        39.88        25.58        16.18        22.49        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       61.05        21.37         0.89        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       27.68        21.07        10.16        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 
       21.60        15.91        15.62         6.74         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 TCGA-5P-A9K8 
       49.58        90.21        22.26        78.64        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       30.48        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       17.49        12.30        19.27        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
       10.82         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
       61.28        50.40        49.84         7.63         7.04         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 
       27.65         1.05        12.43        12.89        11.21        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.95            0.10 
  SETD2 MUTATED SETD2 WILD-TYPE 
          86.76          194.79 
  SETD2 MUTATED SETD2 WILD-TYPE 
         12.905          25.640 
[1] "0.9 - 86.8 (12.9)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "3.5"
D1V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED         5        0         7        3
  SETD2 WILD-TYPE     165       21        42       12
D1V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I               5             165
  STAGE II              0              21
  STAGE III             7              42
  STAGE IV              3              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SETD2 MUTATED     6   1     9
  SETD2 WILD-TYPE 183  31    50
D1V4, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  T1                6             183
  T2                1              31
  T3+T4             9              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  SETD2 MUTATED    4     4
  SETD2 WILD-TYPE 45    21
D1V5, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  N0                4              45
  N1+N2             4              21
[1] 2 2
[1] FALSE
D1V6, binary
                 cls
clus               0  1
  SETD2 MUTATED    6  2
  SETD2 WILD-TYPE 88  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      6    2
  SETD2 WILD-TYPE   88    7
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0             6              88
  1             2               7
[1] 2 2
[1] FALSE
D1V7, binary
                 cls
clus                0   1
  SETD2 MUTATED     3  13
  SETD2 WILD-TYPE  73 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      3   13
  SETD2 WILD-TYPE   73  193
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE             3              73
  MALE              13             193
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              54 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-2Z-A9J3      TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-A8LE      TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-Q2-A5QZ      TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-Y8-A896      TCGA-Y8-A8RY 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     0
  SETD2 WILD-TYPE                                2     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           6    10
  SETD2 WILD-TYPE                        53   190
D1V11, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               6
  BLACK OR AFRICAN AMERICAN                    6              53
  WHITE                                       10             190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                 cls
clus                0   1
  SETD2 MUTATED     0  14
  SETD2 WILD-TYPE  11 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      0   14
  SETD2 WILD-TYPE   11  221
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO            14             221
[1] 2 2
[1] FALSE

Clustering(2) Variable = NF2 MUTATION ANALYSIS
D2V1, survival
               sevent
clus2             0   1
  NF2 MUTATED     8   2
  NF2 WILD-TYPE 230  39
  NF2 MUTATED NF2 WILD-TYPE 
           10           269 
  NF2 MUTATED NF2 WILD-TYPE 
            2            39 
$`NF2 MUTATED`
TCGA-B1-A47M TCGA-B9-4117 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-EV-5902 TCGA-G7-6797 
       21.67         0.46        86.76         8.88        19.00        25.15 
TCGA-GL-7966 TCGA-P4-A5EA TCGA-SX-A7SL TCGA-Y8-A896 
        3.68         6.61        27.06        18.64 

$`NF2 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        49.25        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU 
       16.34        12.13        29.26        19.73        17.75        12.49 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       35.38        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
       20.61         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        17.49        12.30        19.27        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
       80.88        51.19        74.60        34.19        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       90.90        11.05        39.25        71.44        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94        99.12        92.58 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       28.80        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  NF2 MUTATED NF2 WILD-TYPE 
         0.46          0.10 
  NF2 MUTATED NF2 WILD-TYPE 
        86.76        194.79 
  NF2 MUTATED NF2 WILD-TYPE 
        18.82         25.35 
[1] "0.5 - 86.8 (18.8)"  "0.1 - 194.8 (25.4)"
[1] "hr=" "2.3"
D2V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         2        0         6        1
  NF2 WILD-TYPE     168       21        43       14
D2V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             2           168
  STAGE II            0            21
  STAGE III           6            43
  STAGE IV            1            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  NF2 MUTATED     3   1     6
  NF2 WILD-TYPE 186  31    53
D2V4, multiclass
       clus
vv      NF2 MUTATED NF2 WILD-TYPE
  T1              3           186
  T2              1            31
  T3+T4           6            53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1+N2
  NF2 MUTATED    0     3
  NF2 WILD-TYPE 49    22
D2V5, multiclass
       clus
vv      NF2 MUTATED NF2 WILD-TYPE
  N0              0            49
  N1+N2           3            22
[1] 2 2
[1] FALSE
D2V6, binary
               cls
clus             0  1
  NF2 MUTATED    3  1
  NF2 WILD-TYPE 91  8
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      3    1
  NF2 WILD-TYPE   91    8
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           3            91
  1           1             8
[1] 2 2
[1] FALSE
D2V7, binary
               cls
clus              0   1
  NF2 MUTATED     4   6
  NF2 WILD-TYPE  72 200
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      4    6
  NF2 WILD-TYPE   72  200
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           4            72
  MALE             6           200
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF2 MUTATED                                  0     0
  NF2 WILD-TYPE                                2     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED                           3     6
  NF2 WILD-TYPE                        56   194
D2V11, multiclass
                                  clus
vv                                 NF2 MUTATED NF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             6
  BLACK OR AFRICAN AMERICAN                  3            56
  WHITE                                      6           194
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
               cls
clus              0   1
  NF2 MUTATED     0   6
  NF2 WILD-TYPE  11 229
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      0    6
  NF2 WILD-TYPE   11  229
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               0            11
  NOT HISPANIC OR LATINO           6           229
[1] 2 2
[1] FALSE

Clustering(3) Variable = ZNF814 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  ZNF814 MUTATED     7   2
  ZNF814 WILD-TYPE 231  39
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               9              270 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               39 
$`ZNF814 MUTATED`
TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-DW-7840 TCGA-2Z-A9J3 TCGA-5P-A9K8 TCGA-GL-A4EM 
       12.99        11.87         3.75        58.22        43.04         1.05 
TCGA-KV-A6GE TCGA-P4-A5EB TCGA-Y8-A894 
       29.10        99.12        18.64 

$`ZNF814 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       12.26        67.17        61.05        21.37         0.89        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
       35.93        37.55        24.46        13.78        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        59.01       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       15.48        62.93        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC 
      194.79        12.92         3.68        27.65        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.55        10.09        18.41        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94         6.61        92.58 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       39.06        18.64        18.05        25.28         6.02        13.28 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
            1.05             0.10 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           99.12           194.79 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          18.640           25.235 
[1] "1.1 - 99.1 (18.6)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "1.6"
D3V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         5        1         2        0
  ZNF814 WILD-TYPE     165       20        47       15
D3V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                5              165
  STAGE II               1               20
  STAGE III              2               47
  STAGE IV               0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ZNF814 MUTATED     6   1     2
  ZNF814 WILD-TYPE 183  31    57
D3V4, multiclass
       clus
vv      ZNF814 MUTATED ZNF814 WILD-TYPE
  T1                 6              183
  T2                 1               31
  T3+T4              2               57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  ZNF814 MUTATED    0     1
  ZNF814 WILD-TYPE 49    24
D3V5, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1               73 
      TCGA-5P-A9JU       TCGA-B1-A47O       TCGA-B1-A657       TCGA-BQ-5888 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-7056       TCGA-IA-A83W       TCGA-Y8-A8RZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-2Z-A9J1       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93X 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-4A-A93Y       TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A7UZ       TCGA-AL-3466       TCGA-AL-3472 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AL-3473       TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B1-A656       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-DW-7963       TCGA-DZ-6131 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-F9-A8NY       TCGA-F9-A97G       TCGA-G7-6789       TCGA-G7-6793 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-G7-A8LD       TCGA-GL-6846 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-GL-7966       TCGA-GL-A59R       TCGA-GL-A9DC       TCGA-IA-A40U 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537       TCGA-J7-A8I2 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KV-A74V       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-P4-AAVL       TCGA-SX-A71R       TCGA-SX-A7SM       TCGA-SX-A7SP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-UN-AAZ9       TCGA-UZ-A9PM       TCGA-UZ-A9PX 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-Y8-A897 
"ZNF814 WILD-TYPE" 
D3V6, binary
                  cls
clus                0  1
  ZNF814 MUTATED    0  0
  ZNF814 WILD-TYPE 94  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    0
  ZNF814 WILD-TYPE   94    9
D3V7, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     2   7
  ZNF814 WILD-TYPE  74 199
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      2    7
  ZNF814 WILD-TYPE   74  199
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              2               74
  MALE                7              199
[1] 2 2
[1] FALSE
D3V8, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1               75 
      TCGA-2Z-A9JL       TCGA-2Z-A9JT       TCGA-5P-A9JU       TCGA-DW-5560 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7836       TCGA-DW-7837 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7841       TCGA-DW-7842 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-2Z-A9JE 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-2Z-A9JK       TCGA-2Z-A9JN       TCGA-4A-A93W       TCGA-4A-A93X 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-4A-A93Y       TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-EV-5903       TCGA-F9-A7Q0       TCGA-G7-6789       TCGA-G7-6790 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-6796 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LC       TCGA-G7-A8LD       TCGA-G7-A8LE 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-Q2-A5QZ       TCGA-SX-A71R       TCGA-SX-A71S       TCGA-SX-A71U 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A71V       TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SN 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR       TCGA-SX-A7SS 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
D3V9, continuous
D3V10, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               53 
      TCGA-2Z-A9JD       TCGA-DW-5561       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JN 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-A4-A48D 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472       TCGA-AL-7173 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117       TCGA-B9-A69E 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7963       TCGA-F9-A97G       TCGA-G7-6793       TCGA-G7-6795 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-IA-A40U 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E6       TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-WN-AB4C       TCGA-Y8-A896 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-Y8-A8RY 
"ZNF814 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF814 MUTATED                                  0     0
  ZNF814 WILD-TYPE                                2     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF814 MUTATED                           2     7
  ZNF814 WILD-TYPE                        57   193
D3V11, multiclass
                                  clus
vv                                 ZNF814 MUTATED ZNF814 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                6
  BLACK OR AFRICAN AMERICAN                     2               57
  WHITE                                         7              193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     0   9
  ZNF814 WILD-TYPE  11 226
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    9
  ZNF814 WILD-TYPE   11  226
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              9              226
[1] 2 2
[1] FALSE

Clustering(4) Variable = MET MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  MET MUTATED    18   3
  MET WILD-TYPE 220  38
  MET MUTATED MET WILD-TYPE 
           21           258 
  MET MUTATED MET WILD-TYPE 
            3            38 
$`MET MUTATED`
TCGA-A4-7734 TCGA-IA-A83W TCGA-4A-A93W TCGA-5P-A9KA TCGA-A4-7997 TCGA-AL-3472 
        0.89        67.17         0.13        12.99        30.48        66.71 
TCGA-AL-7173 TCGA-B1-7332 TCGA-BQ-5882 TCGA-BQ-7059 TCGA-DZ-6132 TCGA-DZ-6135 
       67.73        37.51        21.63         7.63        80.88        74.60 
TCGA-G7-A8LE TCGA-GL-A59R TCGA-HE-A5NH TCGA-IA-A40U TCGA-IZ-8196 TCGA-MH-A561 
       80.65        12.43        26.01        16.80        21.34        27.65 
TCGA-SX-A71S TCGA-SX-A7SQ TCGA-UZ-A9PJ 
       49.45        41.62        26.20 

$`MET WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-A5Y1 TCGA-AL-3468 
       12.26        67.17        61.05        21.37        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 
       14.63         3.02        61.02        17.95        84.89        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KC TCGA-5P-A9KE 
       78.64        15.48        62.93        43.04        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        7.82         0.23        16.64        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
        9.63        70.19        62.66         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
       49.84         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       51.19        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        23.08        16.90       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        3.68        27.65         1.05        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       81.93        58.19        11.84        56.75        73.25        25.22 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 
       11.41        34.29        27.78        30.38        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        18.02       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  MET MUTATED MET WILD-TYPE 
         0.13          0.10 
  MET MUTATED MET WILD-TYPE 
        80.88        194.79 
  MET MUTATED MET WILD-TYPE 
       27.650        24.675 
[1] "0.1 - 80.9 (27.6)"  "0.1 - 194.8 (24.7)"
[1] "hr=" "1.1"
D4V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  MET MUTATED        14        1         3        1
  MET WILD-TYPE     156       20        46       14
D4V3, multiclass
           clus
vv          MET MUTATED MET WILD-TYPE
  STAGE I            14           156
  STAGE II            1            20
  STAGE III           3            46
  STAGE IV            1            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  MET MUTATED    15   2     4
  MET WILD-TYPE 174  30    55
D4V4, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  T1             15           174
  T2              2            30
  T3+T4           4            55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1+N2
  MET MUTATED    6     1
  MET WILD-TYPE 43    24
D4V5, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  N0              6            43
  N1+N2           1            24
[1] 2 2
[1] FALSE
D4V6, binary
               cls
clus             0  1
  MET MUTATED    9  0
  MET WILD-TYPE 85  9
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      9    0
  MET WILD-TYPE   85    9
   clus
vv  MET MUTATED MET WILD-TYPE
  0           9            85
  1           0             9
[1] 2 2
[1] FALSE
D4V7, binary
               cls
clus              0   1
  MET MUTATED     5  16
  MET WILD-TYPE  71 190
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      5   16
  MET WILD-TYPE   71  190
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           5            71
  MALE            16           190
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                2     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           2    15
  MET WILD-TYPE                        57   185
D4V11, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             6
  BLACK OR AFRICAN AMERICAN                  2            57
  WHITE                                     15           185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
               cls
clus              0   1
  MET MUTATED     1  16
  MET WILD-TYPE  10 219
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      1   16
  MET WILD-TYPE   10  219
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               1            10
  NOT HISPANIC OR LATINO          16           219
[1] 2 2
[1] FALSE

Clustering(5) Variable = NEFH MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  NEFH MUTATED     6   0
  NEFH WILD-TYPE 232  41
  NEFH MUTATED NEFH WILD-TYPE 
             6            273 
  NEFH MUTATED NEFH WILD-TYPE 
             0             41 
$`NEFH MUTATED`
TCGA-B9-A5W8 TCGA-HE-A5NL TCGA-KV-A74V TCGA-SX-A71V TCGA-SX-A7SL TCGA-UZ-A9PK 
       17.23        25.22        11.41        28.80        27.06       117.40 

$`NEFH WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       73.25        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.09        18.41        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SM 
       50.60        14.07        47.90        49.45        44.61        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       18.02        26.20       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  NEFH MUTATED NEFH WILD-TYPE 
         11.41           0.10 
  NEFH MUTATED NEFH WILD-TYPE 
        117.40         194.79 
  NEFH MUTATED NEFH WILD-TYPE 
         26.14          25.15 
[1] "11.4 - 117.4 (26.1)" "0.1 - 194.8 (25.1)" 
[1] "hr="     "9300000"
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         5        1         0        0
  NEFH WILD-TYPE     165       20        49       15
D5V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              5            165
  STAGE II             1             20
  STAGE III            0             49
  STAGE IV             0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  NEFH MUTATED     5   1     0
  NEFH WILD-TYPE 184  31    59
D5V4, multiclass
       clus
vv      NEFH MUTATED NEFH WILD-TYPE
  T1               5            184
  T2               1             31
  T3+T4            0             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  NEFH MUTATED    1     0
  NEFH WILD-TYPE 48    25
D5V5, multiclass
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             1             73 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-2Z-A9J1     TCGA-2Z-A9JO     TCGA-4A-A93W 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7583     TCGA-A4-7585 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A7UZ     TCGA-AL-3466 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B1-A655     TCGA-B1-A656     TCGA-B9-7268     TCGA-BQ-5877 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5889     TCGA-BQ-5890 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-DW-7963 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DZ-6131     TCGA-F9-A8NY     TCGA-F9-A97G     TCGA-G7-6789 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LD 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-GL-6846     TCGA-GL-7966     TCGA-GL-A59R     TCGA-GL-A9DC 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720     TCGA-J7-8537 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-J7-A8I2     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-P4-AAVL     TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-Y8-A897 
"NEFH WILD-TYPE" 
D5V6, binary
                cls
clus              0  1
  NEFH MUTATED    4  0
  NEFH WILD-TYPE 90  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4    0
  NEFH WILD-TYPE   90    9
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            4             90
  1            0              9
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  NEFH MUTATED     0   6
  NEFH WILD-TYPE  76 200
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    6
  NEFH WILD-TYPE   76  200
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            0             76
  MALE              6            200
[1] 2 2
[1] FALSE
D5V8, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2             74 
    TCGA-2Z-A9JL     TCGA-2Z-A9JT     TCGA-5P-A9JU     TCGA-DW-5560 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7836     TCGA-DW-7837 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-7842     TCGA-SX-A71W     TCGA-SX-A7SO     TCGA-UZ-A9PZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9JE     TCGA-2Z-A9JK     TCGA-2Z-A9JN     TCGA-4A-A93W 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7286     TCGA-A4-7828 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-8517     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A48D 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-A6HP     TCGA-AL-3466     TCGA-DW-7963     TCGA-EV-5901 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-F9-A7Q0     TCGA-G7-6789 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-A4TM     TCGA-G7-A8LB     TCGA-G7-A8LC     TCGA-G7-A8LD 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-J7-8537     TCGA-Q2-A5QZ     TCGA-SX-A71R     TCGA-SX-A71S 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A7SM     TCGA-SX-A7SN     TCGA-SX-A7SP 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A7SQ     TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-SX-A7SU 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-UZ-A9PL     TCGA-V9-A7HT 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" 
D5V9, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             1             75 
    TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU     TCGA-B9-A44B 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838     TCGA-GL-A59T 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU     TCGA-SX-A71W 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ     TCGA-2Z-A9J2 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9J5     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9JK     TCGA-2Z-A9JM     TCGA-2Z-A9JN     TCGA-2Z-A9JO 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-5P-A9K3     TCGA-5P-A9KE 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4117     TCGA-B9-7268 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6792 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LB 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-IA-A83S     TCGA-IA-A83V     TCGA-MH-A854     TCGA-MH-A856 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-Q2-A5QZ     TCGA-SX-A71S 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A7SM     TCGA-SX-A7SR     TCGA-SX-A7SS 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX     TCGA-WN-A9G9 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-Y8-A894     TCGA-Y8-A896     TCGA-Y8-A8RY 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
D5V10, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             1             54 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9J3     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6793 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-IA-A40U     TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E6 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SM 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEFH MUTATED                                  0     0
  NEFH WILD-TYPE                                2     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED                           1     3
  NEFH WILD-TYPE                        58   197
D5V11, multiclass
                                  clus
vv                                 NEFH MUTATED NEFH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              6
  BLACK OR AFRICAN AMERICAN                   1             58
  WHITE                                       3            197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                cls
clus               0   1
  NEFH MUTATED     0   4
  NEFH WILD-TYPE  11 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    4
  NEFH WILD-TYPE   11  231
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            4            231
[1] 2 2
[1] FALSE

Clustering(6) Variable = KRAS MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     5   0
  KRAS WILD-TYPE 233  41
  KRAS MUTATED KRAS WILD-TYPE 
             5            274 
  KRAS MUTATED KRAS WILD-TYPE 
             0             41 
$`KRAS MUTATED`
TCGA-2Z-A9JN TCGA-A4-8312 TCGA-BQ-5883 TCGA-GL-A9DC TCGA-MH-A854 
       24.33        23.28        40.83        12.89        17.62 

$`KRAS WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JO TCGA-2Z-A9JP 
       54.64        51.52        38.99        30.71        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
       30.48        29.46        25.64        23.97        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        21.63        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
        1.05        12.43        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       20.25        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  KRAS MUTATED KRAS WILD-TYPE 
         12.89           0.10 
  KRAS MUTATED KRAS WILD-TYPE 
         40.83         194.79 
  KRAS MUTATED KRAS WILD-TYPE 
        23.280         25.265 
[1] "12.9 - 40.8 (23.3)" "0.1 - 194.8 (25.3)"
[1] "hr="     "9200000"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  KRAS MUTATED         5        0         0        0
  KRAS WILD-TYPE     165       21        49       15
D6V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE I              5            165
  STAGE II             0             21
  STAGE III            0             49
  STAGE IV             0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  KRAS MUTATED     5   0     0
  KRAS WILD-TYPE 184  32    59
D6V4, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  T1               5            184
  T2               0             32
  T3+T4            0             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  KRAS MUTATED    1     0
  KRAS WILD-TYPE 48    25
D6V5, multiclass
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             1             73 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-2Z-A9J1     TCGA-2Z-A9JO     TCGA-4A-A93W 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7583     TCGA-A4-7585 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A7UZ     TCGA-AL-3466 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B1-A655     TCGA-B1-A656     TCGA-B9-7268     TCGA-BQ-5877 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5889     TCGA-BQ-5890 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-DW-7963 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DZ-6131     TCGA-F9-A8NY     TCGA-F9-A97G     TCGA-G7-6789 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-6846     TCGA-GL-7966     TCGA-GL-A59R     TCGA-IA-A40U 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KV-A74V     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-P4-AAVL     TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A897 
"KRAS WILD-TYPE" 
D6V6, binary
                cls
clus              0  1
  KRAS MUTATED    1  0
  KRAS WILD-TYPE 93  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1    0
  KRAS WILD-TYPE   93    9
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            1             93
  1            0              9
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  KRAS MUTATED     4   1
  KRAS WILD-TYPE  72 205
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    1
  KRAS WILD-TYPE   72  205
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            4             72
  MALE              1            205
[1] 2 2
[1] FALSE
D6V8, continuous
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2             74 
    TCGA-2Z-A9JL     TCGA-2Z-A9JT     TCGA-5P-A9JU     TCGA-DW-5560 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7836     TCGA-DW-7837 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7842     TCGA-SX-A71W     TCGA-SX-A7SO     TCGA-UZ-A9PZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9JE     TCGA-2Z-A9JK     TCGA-4A-A93W     TCGA-4A-A93X 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-4A-A93Y     TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8517     TCGA-A4-8518 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-8630     TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-F9-A7Q0     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM     TCGA-G7-A8LB 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-A8LC     TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-IA-A40U 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537     TCGA-Q2-A5QZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71R     TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A71V 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SN     TCGA-SX-A7SP 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SQ     TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-SX-A7SU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9PL     TCGA-V9-A7HT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" 
D6V9, continuous
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2             74 
    TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU     TCGA-B9-A44B 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838     TCGA-GL-A59T 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU     TCGA-SX-A71W 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ     TCGA-2Z-A9J2 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9J5     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9JK     TCGA-2Z-A9JM     TCGA-2Z-A9JO     TCGA-4A-A93W 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-4A-A93Y     TCGA-5P-A9K3     TCGA-5P-A9KE     TCGA-A4-8310 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3466 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B9-4115     TCGA-B9-4117     TCGA-B9-7268     TCGA-B9-A69E 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6792     TCGA-G7-6793 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U     TCGA-IA-A83S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IA-A83V     TCGA-MH-A856     TCGA-P4-A5E7     TCGA-P4-A5EB 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UZ-A9PS     TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-Y8-A894 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" 
D6V10, continuous
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2             53 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9J3     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-A4-A48D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472     TCGA-AL-7173 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117     TCGA-B9-A69E 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6793     TCGA-G7-6795 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-IA-A40U 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-MH-A856     TCGA-P4-A5E6     TCGA-Q2-A5QZ     TCGA-SX-A71S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894     TCGA-Y8-A896 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A8RY 
"KRAS WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  0     0
  KRAS WILD-TYPE                                2     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED                           4     1
  KRAS WILD-TYPE                        55   199
D6V11, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              6
  BLACK OR AFRICAN AMERICAN                   4             55
  WHITE                                       1            199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                cls
clus               0   1
  KRAS MUTATED     0   4
  KRAS WILD-TYPE  11 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    4
  KRAS WILD-TYPE   11  231
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            4            231
[1] 2 2
[1] FALSE

Clustering(7) Variable = CUL3 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  CUL3 MUTATED     9   1
  CUL3 WILD-TYPE 229  40
  CUL3 MUTATED CUL3 WILD-TYPE 
            10            269 
  CUL3 MUTATED CUL3 WILD-TYPE 
             1             40 
$`CUL3 MUTATED`
TCGA-2Z-A9JQ TCGA-Y8-A8RZ TCGA-2Z-A9J8 TCGA-5P-A9KA TCGA-A4-A57E TCGA-A4-A5Y0 
       25.58         6.74        91.73        12.99         8.48         8.28 
TCGA-AL-7173 TCGA-B9-A8YI TCGA-BQ-5885 TCGA-P4-A5E6 
       67.73        12.30        30.28        99.78 

$`CUL3 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       34.85        39.88        33.07        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU 
       16.34        12.13        29.26        19.73        17.75        12.49 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       35.38        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       15.62         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
       56.91         4.57        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KC TCGA-5P-A9KE 
       78.64        15.48        62.93        43.04        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3466 
       12.46        16.96        16.31        15.75        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       70.19        66.71        62.66         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        17.49        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 
       27.65        20.25        17.62        31.13        15.48        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  CUL3 MUTATED CUL3 WILD-TYPE 
          6.74           0.10 
  CUL3 MUTATED CUL3 WILD-TYPE 
         99.78         194.79 
  CUL3 MUTATED CUL3 WILD-TYPE 
        19.285         25.220 
[1] "6.7 - 99.8 (19.3)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "1.6"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  CUL3 MUTATED         5        0         2        2
  CUL3 WILD-TYPE     165       21        47       13
D7V3, multiclass
           clus
vv          CUL3 MUTATED CUL3 WILD-TYPE
  STAGE I              5            165
  STAGE II             0             21
  STAGE III            2             47
  STAGE IV             2             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  CUL3 MUTATED     7   1     2
  CUL3 WILD-TYPE 182  31    57
D7V4, multiclass
       clus
vv      CUL3 MUTATED CUL3 WILD-TYPE
  T1               7            182
  T2               1             31
  T3+T4            2             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  CUL3 MUTATED    3     2
  CUL3 WILD-TYPE 46    23
D7V5, multiclass
       clus
vv      CUL3 MUTATED CUL3 WILD-TYPE
  N0               3             46
  N1+N2            2             23
[1] 2 2
[1] FALSE
D7V6, binary
                cls
clus              0  1
  CUL3 MUTATED    2  1
  CUL3 WILD-TYPE 92  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      2    1
  CUL3 WILD-TYPE   92    8
   clus
vv  CUL3 MUTATED CUL3 WILD-TYPE
  0            2             92
  1            1              8
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus               0   1
  CUL3 MUTATED     2   8
  CUL3 WILD-TYPE  74 198
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      2    8
  CUL3 WILD-TYPE   74  198
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  FEMALE            2             74
  MALE              8            198
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "CUL3 MUTATED"          
clus
  CUL3 MUTATED CUL3 WILD-TYPE 
             1             75 
    TCGA-2Z-A9JL     TCGA-2Z-A9JT     TCGA-5P-A9JU     TCGA-DW-5560 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7836     TCGA-DW-7837 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-DW-7842     TCGA-SX-A71W     TCGA-SX-A7SO     TCGA-UZ-A9PZ 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-2Z-A9JE     TCGA-2Z-A9JK     TCGA-2Z-A9JN     TCGA-4A-A93W 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7286     TCGA-A4-7828 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-A4-8517     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A48D 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-A4-A4ZT     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-EV-5903     TCGA-F9-A7Q0     TCGA-G7-6789     TCGA-G7-6790 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-G7-A8LB     TCGA-G7-A8LC     TCGA-G7-A8LD     TCGA-G7-A8LE 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71R     TCGA-SX-A71S     TCGA-SX-A71U 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-SX-A71V     TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SN 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-SX-A7SP     TCGA-SX-A7SQ     TCGA-SX-A7SR     TCGA-SX-A7SS 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
    TCGA-SX-A7SU     TCGA-UZ-A9PL     TCGA-V9-A7HT 
"CUL3 WILD-TYPE" "CUL3 WILD-TYPE" "CUL3 WILD-TYPE" 
D7V9, continuous
D7V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUL3 MUTATED                                  0     0
  CUL3 WILD-TYPE                                2     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUL3 MUTATED                           2     8
  CUL3 WILD-TYPE                        57   192
D7V11, multiclass
                                  clus
vv                                 CUL3 MUTATED CUL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              6
  BLACK OR AFRICAN AMERICAN                   2             57
  WHITE                                       8            192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                cls
clus               0   1
  CUL3 MUTATED     0  10
  CUL3 WILD-TYPE  11 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      0   10
  CUL3 WILD-TYPE   11  225
                        clus
vv                       CUL3 MUTATED CUL3 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO           10            225
[1] 2 2
[1] FALSE

Clustering(8) Variable = PCF11 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  PCF11 MUTATED     9   2
  PCF11 WILD-TYPE 229  39
  PCF11 MUTATED PCF11 WILD-TYPE 
             11             268 
  PCF11 MUTATED PCF11 WILD-TYPE 
              2              39 
$`PCF11 MUTATED`
TCGA-BQ-7058 TCGA-DZ-6134 TCGA-PJ-A8JU TCGA-5P-A9JZ TCGA-B1-5398 TCGA-B9-4617 
       11.28        61.02        12.49        90.21        41.13         1.15 
TCGA-BQ-5876 TCGA-BQ-7050 TCGA-EV-5903 TCGA-IA-A83S TCGA-SX-A71U 
       19.27        61.28        24.89        85.78        44.61 

$`PCF11 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 
       96.92        44.84        26.27        20.12        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
       14.63         3.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-SX-A7SO 
       12.13        29.26        19.73        17.75        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 
       12.82        11.57       106.55        49.58        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
        2.20        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       19.00        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99         2.04        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       14.07        47.90        49.45        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  PCF11 MUTATED PCF11 WILD-TYPE 
           1.15            0.10 
  PCF11 MUTATED PCF11 WILD-TYPE 
          90.21          194.79 
  PCF11 MUTATED PCF11 WILD-TYPE 
         41.130          25.185 
[1] "1.1 - 90.2 (41.1)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "1"  
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PCF11 MUTATED         6        0         2        0
  PCF11 WILD-TYPE     164       21        47       15
D8V3, multiclass
           clus
vv          PCF11 MUTATED PCF11 WILD-TYPE
  STAGE I               6             164
  STAGE II              0              21
  STAGE III             2              47
  STAGE IV              0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PCF11 MUTATED     8   0     2
  PCF11 WILD-TYPE 181  32    57
D8V4, multiclass
       clus
vv      PCF11 MUTATED PCF11 WILD-TYPE
  T1                8             181
  T2                0              32
  T3+T4             2              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  PCF11 MUTATED    2     0
  PCF11 WILD-TYPE 47    25
D8V5, multiclass
[1] "Remove cluster labels:" "PCF11 MUTATED"         
clus
  PCF11 MUTATED PCF11 WILD-TYPE 
              2              72 
     TCGA-5P-A9JU      TCGA-A4-A5Y1      TCGA-B1-A47O      TCGA-B1-A657 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5892      TCGA-BQ-7056      TCGA-IA-A83W 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-Y8-A8RZ      TCGA-2Z-A9J1      TCGA-2Z-A9JO      TCGA-4A-A93W 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7583      TCGA-A4-7585 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7915      TCGA-A4-A57E      TCGA-A4-A7UZ      TCGA-AL-3466 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-A655 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B1-A656      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-7051      TCGA-DW-7963      TCGA-DZ-6131      TCGA-F9-A8NY 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-F9-A97G      TCGA-G7-6789      TCGA-G7-6793      TCGA-G7-6795 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LD      TCGA-GL-6846      TCGA-GL-7966 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-GL-A59R      TCGA-GL-A9DC      TCGA-IA-A40U      TCGA-IA-A40Y 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-J7-6720      TCGA-J7-8537      TCGA-J7-A8I2      TCGA-KV-A74V 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA      TCGA-P4-AAVL 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A71R      TCGA-SX-A7SM      TCGA-SX-A7SP      TCGA-SX-A7SS 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-UN-AAZ9      TCGA-UZ-A9PM      TCGA-UZ-A9PX      TCGA-Y8-A897 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
D8V6, binary
                 cls
clus               0  1
  PCF11 MUTATED    7  0
  PCF11 WILD-TYPE 87  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      7    0
  PCF11 WILD-TYPE   87    9
   clus
vv  PCF11 MUTATED PCF11 WILD-TYPE
  0             7              87
  1             0               9
[1] 2 2
[1] FALSE
D8V7, binary
                 cls
clus                0   1
  PCF11 MUTATED     3   8
  PCF11 WILD-TYPE  73 198
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      3    8
  PCF11 WILD-TYPE   73  198
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  FEMALE             3              73
  MALE               8             198
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "PCF11 MUTATED"         
clus
  PCF11 MUTATED PCF11 WILD-TYPE 
              2              74 
     TCGA-2Z-A9JL      TCGA-2Z-A9JT      TCGA-5P-A9JU      TCGA-DW-5560 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7836      TCGA-DW-7837 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7842      TCGA-SX-A71W      TCGA-SX-A7SO      TCGA-UZ-A9PZ 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-2Z-A9JE      TCGA-2Z-A9JK      TCGA-2Z-A9JN      TCGA-4A-A93W 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7286      TCGA-A4-7828 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A48D 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963      TCGA-EV-5901 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-EV-5902      TCGA-F9-A7Q0      TCGA-G7-6789      TCGA-G7-6790 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-A8LB      TCGA-G7-A8LC      TCGA-G7-A8LD      TCGA-G7-A8LE 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-Q2-A5QZ      TCGA-SX-A71R      TCGA-SX-A71S      TCGA-SX-A71V 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A7SL      TCGA-SX-A7SM      TCGA-SX-A7SN      TCGA-SX-A7SP 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A7SQ      TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-SX-A7SU 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-UZ-A9PL      TCGA-V9-A7HT 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
D8V9, continuous
D8V10, continuous
[1] "Remove cluster labels:" "PCF11 MUTATED"         
clus
  PCF11 MUTATED PCF11 WILD-TYPE 
              2              53 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-SX-A71W 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ      TCGA-2Z-A9J3 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI      TCGA-2Z-A9JN 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y      TCGA-A4-A48D 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472      TCGA-AL-7173 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117      TCGA-B9-A69E 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793      TCGA-G7-6795 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-IA-A40U 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A7SL      TCGA-SX-A7SM      TCGA-SX-A7SR 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS      TCGA-UZ-A9PX 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894      TCGA-Y8-A896 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-Y8-A8RY 
"PCF11 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCF11 MUTATED                                  0     0
  PCF11 WILD-TYPE                                2     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCF11 MUTATED                           1    10
  PCF11 WILD-TYPE                        58   190
D8V11, multiclass
                                  clus
vv                                 PCF11 MUTATED PCF11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               6
  BLACK OR AFRICAN AMERICAN                    1              58
  WHITE                                       10             190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                 cls
clus                0   1
  PCF11 MUTATED     1   8
  PCF11 WILD-TYPE  10 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      1    8
  PCF11 WILD-TYPE   10  227
                        clus
vv                       PCF11 MUTATED PCF11 WILD-TYPE
  HISPANIC OR LATINO                 1              10
  NOT HISPANIC OR LATINO             8             227
[1] 2 2
[1] FALSE

Clustering(9) Variable = BCLAF1 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  BCLAF1 MUTATED     5   1
  BCLAF1 WILD-TYPE 233  40
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               6              273 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               1               40 
$`BCLAF1 MUTATED`
TCGA-DZ-6134 TCGA-Y8-A895 TCGA-A4-7286 TCGA-B9-7268 TCGA-BQ-5878 TCGA-BQ-5893 
       61.02        15.91        18.21        22.06        63.72         7.92 

$`BCLAF1 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
        3.75        14.63         3.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU 
       16.34        12.13        29.26        19.73        17.75        12.49 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A898 
       35.38        41.33        62.83        86.37        21.60        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        67.43        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        1.15        43.99        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76        19.27         8.88        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.82         7.66         0.95         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            7.92             0.10 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           63.72           194.79 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          20.135           25.250 
[1] "7.9 - 63.7 (20.1)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "1.2"
D9V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  BCLAF1 MUTATED         2        1         1        1
  BCLAF1 WILD-TYPE     168       20        48       14
D9V3, multiclass
           clus
vv          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  STAGE I                2              168
  STAGE II               1               20
  STAGE III              1               48
  STAGE IV               1               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  BCLAF1 MUTATED     2   1     3
  BCLAF1 WILD-TYPE 187  31    56
D9V4, multiclass
       clus
vv      BCLAF1 MUTATED BCLAF1 WILD-TYPE
  T1                 2              187
  T2                 1               31
  T3+T4              3               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  BCLAF1 MUTATED    1     2
  BCLAF1 WILD-TYPE 48    23
D9V5, multiclass
       clus
vv      BCLAF1 MUTATED BCLAF1 WILD-TYPE
  N0                 1               48
  N1+N2              2               23
[1] 2 2
[1] FALSE
D9V6, binary
                  cls
clus                0  1
  BCLAF1 MUTATED    2  1
  BCLAF1 WILD-TYPE 92  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      2    1
  BCLAF1 WILD-TYPE   92    8
   clus
vv  BCLAF1 MUTATED BCLAF1 WILD-TYPE
  0              2               92
  1              1                8
[1] 2 2
[1] FALSE
D9V7, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     1   5
  BCLAF1 WILD-TYPE  75 201
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      1    5
  BCLAF1 WILD-TYPE   75  201
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE              1               75
  MALE                5              201
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:" "BCLAF1 MUTATED"        
clus
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               1               75 
      TCGA-2Z-A9JL       TCGA-2Z-A9JT       TCGA-5P-A9JU       TCGA-DW-5560 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7836       TCGA-DW-7837 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DW-7842       TCGA-SX-A71W       TCGA-SX-A7SO       TCGA-UZ-A9PZ 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN       TCGA-4A-A93W 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7828       TCGA-A4-8098 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EV-5903       TCGA-F9-A7Q0       TCGA-G7-6789       TCGA-G7-6790 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-6796 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LC       TCGA-G7-A8LD       TCGA-G7-A8LE 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-Q2-A5QZ       TCGA-SX-A71R       TCGA-SX-A71S       TCGA-SX-A71U 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A71V       TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SN 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR       TCGA-SX-A7SS 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
D9V9, continuous
[1] "Remove cluster labels:" "BCLAF1 MUTATED"        
clus
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               1               75 
      TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU       TCGA-B9-A44B 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838       TCGA-GL-A59T 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU       TCGA-SX-A71W 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ       TCGA-2Z-A9J2 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-2Z-A9J5       TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-2Z-A9JK       TCGA-2Z-A9JM       TCGA-2Z-A9JN       TCGA-2Z-A9JO 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-5P-A9K3       TCGA-5P-A9KE 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173       TCGA-B1-A654 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117       TCGA-B9-A69E 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DW-7963       TCGA-F9-A97G       TCGA-G7-6792       TCGA-G7-6793 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-A8LE       TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U       TCGA-IA-A83S 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-IA-A83V       TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E7 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-P4-A5EB       TCGA-Q2-A5QZ       TCGA-SX-A71S       TCGA-SX-A71U 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SR       TCGA-SX-A7SS 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-UZ-A9PM       TCGA-UZ-A9PS       TCGA-UZ-A9PX       TCGA-WN-A9G9 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-Y8-A894       TCGA-Y8-A896       TCGA-Y8-A8RY 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
D9V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCLAF1 MUTATED                                  0     0
  BCLAF1 WILD-TYPE                                2     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BCLAF1 MUTATED                           0     6
  BCLAF1 WILD-TYPE                        59   194
D9V11, multiclass
                                  clus
vv                                 BCLAF1 MUTATED BCLAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                6
  BLACK OR AFRICAN AMERICAN                     0               59
  WHITE                                         6              194
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     0   4
  BCLAF1 WILD-TYPE  11 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      0    4
  BCLAF1 WILD-TYPE   11  231
                        clus
vv                       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              4              231
[1] 2 2
[1] FALSE

Clustering(10) Variable = PAM MUTATION ANALYSIS
D10V1, survival
               sevent
clus2             0   1
  PAM MUTATED     3   0
  PAM WILD-TYPE 235  41
  PAM MUTATED PAM WILD-TYPE 
            3           276 
  PAM MUTATED PAM WILD-TYPE 
            0            41 
$`PAM MUTATED`
TCGA-HE-A5NI TCGA-IA-A40U TCGA-P4-A5E6 
       11.84        16.80        99.78 

$`PAM WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NJ 
       11.21        16.31        81.93        58.19        26.01        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       73.25        25.22        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  PAM MUTATED PAM WILD-TYPE 
        11.84          0.10 
  PAM MUTATED PAM WILD-TYPE 
        99.78        194.79 
  PAM MUTATED PAM WILD-TYPE 
       16.800        25.235 
[1] "11.8 - 99.8 (16.8)" "0.1 - 194.8 (25.2)"
[1] "hr="     "9300000"
D10V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  PAM MUTATED         1        0         2        0
  PAM WILD-TYPE     169       21        47       15
D10V3, multiclass
           clus
vv          PAM MUTATED PAM WILD-TYPE
  STAGE I             1           169
  STAGE II            0            21
  STAGE III           2            47
  STAGE IV            0            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  PAM MUTATED     2   0     1
  PAM WILD-TYPE 187  32    58
D10V4, multiclass
       clus
vv      PAM MUTATED PAM WILD-TYPE
  T1              2           187
  T2              0            32
  T3+T4           1            58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1+N2
  PAM MUTATED    1     1
  PAM WILD-TYPE 48    24
D10V5, multiclass
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2            72 
   TCGA-5P-A9JU    TCGA-A4-A5Y1    TCGA-B1-A47O    TCGA-B1-A657    TCGA-BQ-5888 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5892    TCGA-BQ-7056    TCGA-IA-A83W    TCGA-Y8-A8RZ    TCGA-2Z-A9J1 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JO    TCGA-4A-A93W    TCGA-4A-A93X    TCGA-4A-A93Y    TCGA-A4-7583 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7585    TCGA-A4-7915    TCGA-A4-A57E    TCGA-A4-A7UZ    TCGA-AL-3466 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173    TCGA-B1-5398    TCGA-B1-A655 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A656    TCGA-B9-7268    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5882    TCGA-BQ-5885    TCGA-BQ-5887    TCGA-BQ-5889 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7045 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7048    TCGA-BQ-7050    TCGA-BQ-7051    TCGA-DW-7963    TCGA-DZ-6131 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-F9-A8NY    TCGA-F9-A97G    TCGA-G7-6789    TCGA-G7-6793    TCGA-G7-6795 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-A8LD    TCGA-GL-6846    TCGA-GL-7966    TCGA-GL-A59R 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-A9DC    TCGA-IA-A40Y    TCGA-J7-6720    TCGA-J7-8537    TCGA-J7-A8I2 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KV-A74V    TCGA-P4-A5E8    TCGA-P4-A5EA    TCGA-P4-AAVL    TCGA-SX-A71R 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SM    TCGA-SX-A7SP    TCGA-SX-A7SS    TCGA-UN-AAZ9    TCGA-UZ-A9PM 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PX    TCGA-Y8-A897 
"PAM WILD-TYPE" "PAM WILD-TYPE" 
D10V6, binary
               cls
clus             0  1
  PAM MUTATED    1  0
  PAM WILD-TYPE 93  9
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      1    0
  PAM WILD-TYPE   93    9
   clus
vv  PAM MUTATED PAM WILD-TYPE
  0           1            93
  1           0             9
[1] 2 2
[1] FALSE
D10V7, binary
               cls
clus              0   1
  PAM MUTATED     0   3
  PAM WILD-TYPE  76 203
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    3
  PAM WILD-TYPE   76  203
        clus
vv       PAM MUTATED PAM WILD-TYPE
  FEMALE           0            76
  MALE             3           203
[1] 2 2
[1] FALSE
D10V8, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            1            75 
   TCGA-2Z-A9JL    TCGA-2Z-A9JT    TCGA-5P-A9JU    TCGA-DW-5560    TCGA-DW-5561 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7836    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-SX-A71W    TCGA-SX-A7SO 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PZ    TCGA-2Z-A9JE    TCGA-2Z-A9JK    TCGA-2Z-A9JN    TCGA-4A-A93W 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-4A-A93X    TCGA-4A-A93Y    TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8098 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312    TCGA-A4-8517    TCGA-A4-8518 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8630    TCGA-A4-A48D    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-7963    TCGA-EV-5901 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-F9-A7Q0    TCGA-G7-6789    TCGA-G7-6790 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-G7-A8LB    TCGA-G7-A8LC 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-IA-A40X    TCGA-IA-A40Y    TCGA-J7-8537 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Q2-A5QZ    TCGA-SX-A71R    TCGA-SX-A71S    TCGA-SX-A71U    TCGA-SX-A71V 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SL    TCGA-SX-A7SM    TCGA-SX-A7SN    TCGA-SX-A7SP    TCGA-SX-A7SQ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SR    TCGA-SX-A7SS    TCGA-SX-A7SU    TCGA-UZ-A9PL    TCGA-V9-A7HT 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
D10V9, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2            74 
   TCGA-2Z-A9JD    TCGA-2Z-A9JQ    TCGA-5P-A9JU    TCGA-B9-A44B    TCGA-DW-5561 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7838    TCGA-GL-A59T    TCGA-IZ-A6M8    TCGA-PJ-A5Z9 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-PJ-A8JU    TCGA-SX-A71W    TCGA-UZ-A9PO    TCGA-UZ-A9PR    TCGA-Y8-A8RZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9J2    TCGA-2Z-A9J5    TCGA-2Z-A9J7    TCGA-2Z-A9J8    TCGA-2Z-A9JI 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JK    TCGA-2Z-A9JM    TCGA-2Z-A9JN    TCGA-2Z-A9JO    TCGA-4A-A93W 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-4A-A93Y    TCGA-5P-A9K3    TCGA-5P-A9KE    TCGA-A4-8310    TCGA-A4-A48D 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-7173 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4117    TCGA-B9-7268 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A69E    TCGA-DW-7963    TCGA-F9-A97G    TCGA-G7-6792    TCGA-G7-6793 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-7501    TCGA-G7-A8LB    TCGA-G7-A8LD    TCGA-G7-A8LE 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-7773    TCGA-GL-A9DD    TCGA-HE-A5NJ    TCGA-HE-A5NK    TCGA-IA-A83S 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IA-A83V    TCGA-MH-A854    TCGA-MH-A856    TCGA-P4-A5E7    TCGA-P4-A5EB 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Q2-A5QZ    TCGA-SX-A71S    TCGA-SX-A71U    TCGA-SX-A7SL    TCGA-SX-A7SM 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SR    TCGA-SX-A7SS    TCGA-UZ-A9PM    TCGA-UZ-A9PS    TCGA-UZ-A9PX 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-WN-A9G9    TCGA-Y8-A894    TCGA-Y8-A896    TCGA-Y8-A8RY 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
D10V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAM MUTATED                                  0     0
  PAM WILD-TYPE                                2     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PAM MUTATED                           1     1
  PAM WILD-TYPE                        58   199
D10V11, multiclass
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2           265 
   TCGA-2Z-A9JD    TCGA-2Z-A9JJ    TCGA-2Z-A9JL    TCGA-2Z-A9JQ    TCGA-2Z-A9JS 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JT    TCGA-5P-A9JU    TCGA-5P-A9JV    TCGA-A4-7288    TCGA-A4-7584 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7734    TCGA-A4-A5Y1    TCGA-AL-3468    TCGA-AL-A5DJ    TCGA-B1-A47M 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A47O    TCGA-B1-A657    TCGA-B3-A6W5    TCGA-B9-5155    TCGA-B9-A44B 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A5W7    TCGA-BQ-5886    TCGA-BQ-5888    TCGA-BQ-5892    TCGA-BQ-7046 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7049    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058    TCGA-DW-5560 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7836    TCGA-DW-7837    TCGA-DW-7838 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6134 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-A59T    TCGA-IA-A83W    TCGA-IZ-A6M8    TCGA-MH-A855    TCGA-MH-A857 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-PJ-A5Z8    TCGA-PJ-A5Z9    TCGA-PJ-A8JU    TCGA-SX-A71W    TCGA-SX-A7SO 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PO    TCGA-UZ-A9PR    TCGA-UZ-A9PZ    TCGA-Y8-A895    TCGA-Y8-A898 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Y8-A8RZ    TCGA-2K-A9WE    TCGA-2Z-A9J1    TCGA-2Z-A9J2    TCGA-2Z-A9J3 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9J5    TCGA-2Z-A9J6    TCGA-2Z-A9J7    TCGA-2Z-A9J8    TCGA-2Z-A9JE 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JG    TCGA-2Z-A9JI    TCGA-2Z-A9JK    TCGA-2Z-A9JM    TCGA-2Z-A9JN 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JO    TCGA-2Z-A9JP    TCGA-2Z-A9JR    TCGA-4A-A93W    TCGA-4A-A93X 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-4A-A93Y    TCGA-5P-A9JW    TCGA-5P-A9JY    TCGA-5P-A9JZ    TCGA-5P-A9K0 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-5P-A9K2    TCGA-5P-A9K3    TCGA-5P-A9K6    TCGA-5P-A9K8    TCGA-5P-A9KA 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-5P-A9KC    TCGA-5P-A9KE    TCGA-5P-A9KH    TCGA-A4-7286    TCGA-A4-7287 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7583    TCGA-A4-7585    TCGA-A4-7732    TCGA-A4-7828    TCGA-A4-7915 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7996    TCGA-A4-7997    TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8311 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8312    TCGA-A4-8515    TCGA-A4-8517    TCGA-A4-8518    TCGA-A4-8630 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A48D    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU    TCGA-A4-A5XZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A5Y0    TCGA-A4-A6HP    TCGA-A4-A772    TCGA-A4-A7UZ    TCGA-AL-3466 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173    TCGA-AT-A5NU 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-5398    TCGA-B1-7332    TCGA-B1-A47N    TCGA-B1-A654    TCGA-B1-A655 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A656    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B3-8121    TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-4617    TCGA-B9-5156    TCGA-B9-7268    TCGA-B9-A5W8 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A5W9    TCGA-B9-A69E    TCGA-B9-A8YH    TCGA-B9-A8YI    TCGA-BQ-5875 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5881    TCGA-BQ-5883    TCGA-BQ-5884    TCGA-BQ-5885    TCGA-BQ-5887 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5889    TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5893    TCGA-BQ-7044 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7048    TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7053 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-7963 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DZ-6131    TCGA-DZ-6133    TCGA-EV-5901    TCGA-EV-5902    TCGA-EV-5903 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-F9-A4JJ    TCGA-F9-A7Q0    TCGA-F9-A7VF    TCGA-F9-A8NY    TCGA-F9-A97G 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-A8LB    TCGA-G7-A8LC    TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-GL-6846 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-7773    TCGA-GL-7966    TCGA-GL-8500    TCGA-GL-A4EM    TCGA-GL-A59R 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-A9DC    TCGA-GL-A9DD    TCGA-GL-A9DE    TCGA-IA-A40X    TCGA-IA-A40Y 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IA-A83S    TCGA-IA-A83T    TCGA-IA-A83V    TCGA-IZ-8195    TCGA-IZ-8196 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IZ-A6M9    TCGA-J7-6720    TCGA-J7-8537    TCGA-J7-A8I2    TCGA-KV-A6GD 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KV-A6GE    TCGA-KV-A74V    TCGA-MH-A55W    TCGA-MH-A55Z    TCGA-MH-A560 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-MH-A561    TCGA-MH-A562    TCGA-MH-A854    TCGA-MH-A856    TCGA-O9-A75Z 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-P4-A5E7    TCGA-P4-A5E8    TCGA-P4-A5EA    TCGA-P4-A5EB    TCGA-P4-A5ED 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-P4-AAVL    TCGA-P4-AAVM    TCGA-Q2-A5QZ    TCGA-SX-A71R    TCGA-SX-A71S 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A71U    TCGA-SX-A71V    TCGA-SX-A7SM    TCGA-SX-A7SN    TCGA-SX-A7SP 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SQ    TCGA-SX-A7SR    TCGA-SX-A7SS    TCGA-UN-AAZ9    TCGA-UZ-A9PJ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PK    TCGA-UZ-A9PL    TCGA-UZ-A9PM    TCGA-UZ-A9PN    TCGA-UZ-A9PP 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PS    TCGA-UZ-A9PU    TCGA-UZ-A9PV    TCGA-UZ-A9PX    TCGA-UZ-A9Q0 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9Q1    TCGA-V9-A7HT    TCGA-WN-A9G9    TCGA-WN-AB4C    TCGA-Y8-A894 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Y8-A896    TCGA-Y8-A897    TCGA-Y8-A8RY    TCGA-Y8-A8S0    TCGA-Y8-A8S1 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
D10V12, binary
               cls
clus              0   1
  PAM MUTATED     0   2
  PAM WILD-TYPE  11 233
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    2
  PAM WILD-TYPE   11  233
                        clus
vv                       PAM MUTATED PAM WILD-TYPE
  HISPANIC OR LATINO               0            11
  NOT HISPANIC OR LATINO           2           233
[1] 2 2
[1] FALSE

Clustering(11) Variable = SMARCB1 MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED     6   0
  SMARCB1 WILD-TYPE 232  41
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                6               273 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                0                41 
$`SMARCB1 MUTATED`
TCGA-5P-A9JU TCGA-B1-A47M TCGA-5P-A9KC TCGA-BQ-5876 TCGA-BQ-7048 TCGA-GL-6846 
       12.26        21.67        12.39        19.27        93.34       194.79 

$`SMARCB1 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       49.25        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        86.76         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
      123.62        48.26        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            12.26              0.10 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           194.79            129.86 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            20.47             25.25 
[1] "12.3 - 194.8 (20.5)" "0.1 - 129.9 (25.2)" 
[1] "hr="     "2.6e+07"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SMARCB1 MUTATED         1        0         3        1
  SMARCB1 WILD-TYPE     169       21        46       14
D11V3, multiclass
           clus
vv          SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                 1               169
  STAGE II                0                21
  STAGE III               3                46
  STAGE IV                1                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  SMARCB1 MUTATED     2   0     4
  SMARCB1 WILD-TYPE 187  32    55
D11V4, multiclass
       clus
vv      SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1                  2               187
  T2                  0                32
  T3+T4               4                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  SMARCB1 MUTATED    2     1
  SMARCB1 WILD-TYPE 47    24
D11V5, multiclass
       clus
vv      SMARCB1 MUTATED SMARCB1 WILD-TYPE
  N0                  2                47
  N1+N2               1                24
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  SMARCB1 MUTATED    3  0
  SMARCB1 WILD-TYPE 91  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      3    0
  SMARCB1 WILD-TYPE   91    9
   clus
vv  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  0               3                91
  1               0                 9
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     1   5
  SMARCB1 WILD-TYPE  75 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      1    5
  SMARCB1 WILD-TYPE   75  201
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE               1                75
  MALE                 5               201
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "SMARCB1 MUTATED"       
clus
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                1                75 
       TCGA-2Z-A9JL        TCGA-2Z-A9JT        TCGA-DW-5560        TCGA-DW-5561 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A71W        TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-2Z-A9JE 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-2Z-A9JK        TCGA-2Z-A9JN        TCGA-4A-A93W        TCGA-4A-A93X 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-EV-5903        TCGA-F9-A7Q0        TCGA-G7-6789        TCGA-G7-6790 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A7SU        TCGA-UZ-A9PL        TCGA-V9-A7HT 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
D11V9, continuous
[1] "Remove cluster labels:" "SMARCB1 MUTATED"       
clus
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                1                75 
       TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-B9-A44B        TCGA-DW-5561 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7838        TCGA-GL-A59T        TCGA-IZ-A6M8 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-PJ-A8JU        TCGA-SX-A71W        TCGA-UZ-A9PO 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-2Z-A9J2        TCGA-2Z-A9J5 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JK 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-2Z-A9JM        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-5P-A9K3        TCGA-5P-A9KE        TCGA-A4-8310 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3466 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-B9-4115        TCGA-B9-4117        TCGA-B9-7268        TCGA-B9-A69E 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-6792        TCGA-G7-6793 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LD 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U        TCGA-IA-A83S 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IA-A83V        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
D11V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCB1 MUTATED                                  0     0
  SMARCB1 WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCB1 MUTATED                           1     5
  SMARCB1 WILD-TYPE                        58   195
D11V11, multiclass
                                  clus
vv                                 SMARCB1 MUTATED SMARCB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                58
  WHITE                                          5               195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     0   5
  SMARCB1 WILD-TYPE  11 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0    5
  SMARCB1 WILD-TYPE   11  230
                        clus
vv                       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               5               230
[1] 2 2
[1] FALSE

Clustering(12) Variable = KDM6A MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     9   1
  KDM6A WILD-TYPE 229  40
  KDM6A MUTATED KDM6A WILD-TYPE 
             10             269 
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              40 
$`KDM6A MUTATED`
TCGA-A4-7584 TCGA-BQ-5886 TCGA-5P-A9K0 TCGA-5P-A9KE TCGA-A4-A48D TCGA-HE-7129 
       21.37        26.04        22.26        27.09        12.46        81.93 
TCGA-HE-7130 TCGA-J7-A8I2 TCGA-SX-A7SP TCGA-SX-A7SS 
       58.19        10.09        16.31        53.10 

$`KDM6A WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       12.26        67.17        61.05         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       11.87        19.23        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.89        11.21        16.31        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.55        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR 
       28.80        27.06        11.93        19.00        41.62        26.47 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  KDM6A MUTATED KDM6A WILD-TYPE 
          10.09            0.10 
  KDM6A MUTATED KDM6A WILD-TYPE 
          81.93          194.79 
  KDM6A MUTATED KDM6A WILD-TYPE 
          24.15           25.22 
[1] "10.1 - 81.9 (24.1)" "0.1 - 194.8 (25.2)"
[1] "hr=" "1.5"
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         5        1         2        0
  KDM6A WILD-TYPE     165       20        47       15
D12V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               5             165
  STAGE II              1              20
  STAGE III             2              47
  STAGE IV              0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  KDM6A MUTATED     7   1     2
  KDM6A WILD-TYPE 182  31    57
D12V4, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  T1                7             182
  T2                1              31
  T3+T4             2              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  KDM6A MUTATED    3     0
  KDM6A WILD-TYPE 46    25
D12V5, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  N0                3              46
  N1+N2             0              25
[1] 2 2
[1] FALSE
D12V6, binary
                 cls
clus               0  1
  KDM6A MUTATED    7  0
  KDM6A WILD-TYPE 87  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      7    0
  KDM6A WILD-TYPE   87    9
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             7              87
  1             0               9
[1] 2 2
[1] FALSE
D12V7, binary
                 cls
clus                0   1
  KDM6A MUTATED     2   8
  KDM6A WILD-TYPE  74 198
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      2    8
  KDM6A WILD-TYPE   74  198
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             2              74
  MALE               8             198
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              2              53 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-2Z-A9J3      TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472      TCGA-AL-7173 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117      TCGA-B9-A69E 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793      TCGA-G7-6795 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-IA-A40U 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-UZ-A9PM      TCGA-UZ-A9PS      TCGA-UZ-A9PX 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894      TCGA-Y8-A896 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-Y8-A8RY 
"KDM6A WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  0     1
  KDM6A WILD-TYPE                                2     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           2     5
  KDM6A WILD-TYPE                        57   195
D12V11, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               5
  BLACK OR AFRICAN AMERICAN                    2              57
  WHITE                                        5             195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                 cls
clus                0   1
  KDM6A MUTATED     0   7
  KDM6A WILD-TYPE  11 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    7
  KDM6A WILD-TYPE   11  228
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             7             228
[1] 2 2
[1] FALSE

Clustering(13) Variable = AR MUTATION ANALYSIS
D13V1, survival
              sevent
clus2            0   1
  AR MUTATED    10   3
  AR WILD-TYPE 228  38
  AR MUTATED AR WILD-TYPE 
          13          266 
  AR MUTATED AR WILD-TYPE 
           3           38 
$`AR MUTATED`
TCGA-2Z-A9J3 TCGA-2Z-A9JO TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-A4-A5Y0 TCGA-B1-A656 
       58.22        31.20       106.55        90.21         8.28        20.32 
TCGA-G7-A8LD TCGA-GL-A9DC TCGA-IA-A83T TCGA-SX-A71U TCGA-UZ-A9PL TCGA-UZ-A9Q1 
       16.90        12.89        88.24        44.61       103.63        51.35 
TCGA-Y8-A8S0 
        6.02 

$`AR WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JP TCGA-2Z-A9JR 
       51.52        38.99        30.71        24.33        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 
        0.13        12.82        11.57        49.58        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP 
       12.46        16.96         8.48        16.31        15.75        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 
       41.13        37.51        36.49        20.25        16.77        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        23.08        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DD TCGA-GL-A9DE 
        3.68        27.65         1.05        12.43        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83V 
       25.22        16.80        19.99         2.04        85.78        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL 
       50.60        14.07        47.90        49.45        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        18.02        26.20       117.40       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S1 
       25.28        13.28 

  AR MUTATED AR WILD-TYPE 
        6.02         0.10 
  AR MUTATED AR WILD-TYPE 
      106.55       194.79 
  AR MUTATED AR WILD-TYPE 
       44.61        25.02 
[1] "6.0 - 106.5 (44.6)" "0.1 - 194.8 (25.0)"
[1] "hr=" "1"  
D13V2, continuous
              vv
clus           STAGE I STAGE II STAGE III STAGE IV
  AR MUTATED         7        2         1        0
  AR WILD-TYPE     163       19        48       15
D13V3, multiclass
           clus
vv          AR MUTATED AR WILD-TYPE
  STAGE I            7          163
  STAGE II           2           19
  STAGE III          1           48
  STAGE IV           0           15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2 T3+T4
  AR MUTATED     9   2     1
  AR WILD-TYPE 180  30    58
D13V4, multiclass
       clus
vv      AR MUTATED AR WILD-TYPE
  T1             9          180
  T2             2           30
  T3+T4          1           58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           N0 N1+N2
  AR MUTATED    3     1
  AR WILD-TYPE 46    24
D13V5, multiclass
       clus
vv      AR MUTATED AR WILD-TYPE
  N0             3           46
  N1+N2          1           24
[1] 2 2
[1] FALSE
D13V6, binary
              cls
clus            0  1
  AR MUTATED    2  0
  AR WILD-TYPE 92  9
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      2    0
  AR WILD-TYPE   92    9
   clus
vv  AR MUTATED AR WILD-TYPE
  0          2           92
  1          0            9
[1] 2 2
[1] FALSE
D13V7, binary
              cls
clus             0   1
  AR MUTATED     5   8
  AR WILD-TYPE  71 198
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      5    8
  AR WILD-TYPE   71  198
        clus
vv       AR MUTATED AR WILD-TYPE
  FEMALE          5           71
  MALE            8          198
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  AR MUTATED                                  0     0                         1
  AR WILD-TYPE                                2     6                        58
              vv
clus           WHITE
  AR MUTATED      12
  AR WILD-TYPE   188
D13V11, multiclass
                                  clus
vv                                 AR MUTATED AR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            2
  ASIAN                                     0            6
  BLACK OR AFRICAN AMERICAN                 1           58
  WHITE                                    12          188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
              cls
clus             0   1
  AR MUTATED     0  13
  AR WILD-TYPE  11 222
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      0   13
  AR WILD-TYPE   11  222
                        clus
vv                       AR MUTATED AR WILD-TYPE
  HISPANIC OR LATINO              0           11
  NOT HISPANIC OR LATINO         13          222
[1] 2 2
[1] FALSE

Clustering(14) Variable = TP53 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  TP53 MUTATED     4   3
  TP53 WILD-TYPE 234  38
  TP53 MUTATED TP53 WILD-TYPE 
             7            272 
  TP53 MUTATED TP53 WILD-TYPE 
             3             38 
$`TP53 MUTATED`
TCGA-5P-A9K3 TCGA-5P-A9KH TCGA-A4-A57E TCGA-B1-A655 TCGA-B3-4104 TCGA-BQ-5881 
       15.48        67.43         8.48        16.77        34.49        47.80 
TCGA-BQ-5893 
        7.92 

$`TP53 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 TCGA-5P-A9K8 
       49.58        90.21        22.26        78.64        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.99        12.39        27.09        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46        16.96        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        29.03        30.58        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         0.95         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  TP53 MUTATED TP53 WILD-TYPE 
          7.92           0.10 
  TP53 MUTATED TP53 WILD-TYPE 
         67.43         194.79 
  TP53 MUTATED TP53 WILD-TYPE 
        16.770         25.235 
[1] "7.9 - 67.4 (16.8)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "4.1"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         2        1         0        2
  TP53 WILD-TYPE     168       20        49       13
D14V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              2            168
  STAGE II             1             20
  STAGE III            0             49
  STAGE IV             2             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  TP53 MUTATED     3   3     1
  TP53 WILD-TYPE 186  29    58
D14V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1               3            186
  T2               3             29
  T3+T4            1             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  TP53 MUTATED    2     1
  TP53 WILD-TYPE 47    24
D14V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  N0               2             47
  N1+N2            1             24
[1] 2 2
[1] FALSE
D14V6, binary
                cls
clus              0  1
  TP53 MUTATED    3  2
  TP53 WILD-TYPE 91  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3    2
  TP53 WILD-TYPE   91    7
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            3             91
  1            2              7
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus               0   1
  TP53 MUTATED     1   6
  TP53 WILD-TYPE  75 200
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1    6
  TP53 WILD-TYPE   75  200
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            1             75
  MALE              6            200
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             1             75 
    TCGA-2Z-A9JL     TCGA-2Z-A9JT     TCGA-5P-A9JU     TCGA-DW-5560 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7836     TCGA-DW-7837 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DW-7842     TCGA-SX-A71W     TCGA-SX-A7SO     TCGA-UZ-A9PZ 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-2Z-A9JE     TCGA-2Z-A9JK     TCGA-2Z-A9JN     TCGA-4A-A93W 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7286     TCGA-A4-7828 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A4-8517     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A48D 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A4-A4ZT     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EV-5903     TCGA-F9-A7Q0     TCGA-G7-6789     TCGA-G7-6790 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-G7-A8LB     TCGA-G7-A8LC     TCGA-G7-A8LD     TCGA-G7-A8LE 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71R     TCGA-SX-A71S     TCGA-SX-A71U 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-SX-A71V     TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SN 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-SX-A7SP     TCGA-SX-A7SQ     TCGA-SX-A7SR     TCGA-SX-A7SS 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-SX-A7SU     TCGA-UZ-A9PL     TCGA-V9-A7HT 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
D14V9, continuous
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             2             74 
    TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU     TCGA-B9-A44B 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838     TCGA-GL-A59T 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU     TCGA-SX-A71W 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ     TCGA-2Z-A9J2 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-2Z-A9J5     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-2Z-A9JK     TCGA-2Z-A9JM     TCGA-2Z-A9JN     TCGA-2Z-A9JO 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-5P-A9KE     TCGA-A4-8310 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4115 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-7268     TCGA-B9-A69E     TCGA-DW-7963 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-F9-A97G     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-HE-A5NJ 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-HE-A5NK     TCGA-IA-A40U     TCGA-IA-A83S     TCGA-IA-A83V 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E7     TCGA-P4-A5EB 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-UZ-A9PS     TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-Y8-A894 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" 
D14V10, continuous
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             1             54 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-2Z-A9J3     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A5Y0     TCGA-AL-3472     TCGA-AL-7173 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117     TCGA-B9-A69E 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6793     TCGA-G7-6795 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-IA-A40U 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E6     TCGA-Q2-A5QZ 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  0     0
  TP53 WILD-TYPE                                2     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                           0     7
  TP53 WILD-TYPE                        59   193
D14V11, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              6
  BLACK OR AFRICAN AMERICAN                   0             59
  WHITE                                       7            193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                cls
clus               0   1
  TP53 MUTATED     0   7
  TP53 WILD-TYPE  11 228
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0    7
  TP53 WILD-TYPE   11  228
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            7            228
[1] 2 2
[1] FALSE

Clustering(15) Variable = KRTAP4-5 MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                  0   1
  KRTAP4-5 MUTATED     4   1
  KRTAP4-5 WILD-TYPE 234  40
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 5                274 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 1                 40 
$`KRTAP4-5 MUTATED`
TCGA-2K-A9WE TCGA-A4-7732 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-P4-A5E8 
        7.04        19.13        17.49        12.30        42.94 

$`KRTAP4-5 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.91        15.62         6.74        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
        0.10        35.18         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
              7.04               0.10 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
             42.94             194.79 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
            17.490             25.265 
[1] "7.0 - 42.9 (17.5)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "2.6"
D15V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KRTAP4-5 MUTATED         2        1         1        0
  KRTAP4-5 WILD-TYPE     168       20        48       15
D15V3, multiclass
           clus
vv          KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  STAGE I                  2                168
  STAGE II                 1                 20
  STAGE III                1                 48
  STAGE IV                 0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  KRTAP4-5 MUTATED     2   3     0
  KRTAP4-5 WILD-TYPE 187  29    59
D15V4, multiclass
       clus
vv      KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  T1                   2                187
  T2                   3                 29
  T3+T4                0                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  KRTAP4-5 MUTATED    0     1
  KRTAP4-5 WILD-TYPE 49    24
D15V5, multiclass
[1] "Remove cluster labels:" "KRTAP4-5 MUTATED"      
clus
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 1                 73 
        TCGA-5P-A9JU         TCGA-A4-A5Y1         TCGA-B1-A47O 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-B1-A657         TCGA-BQ-5888         TCGA-BQ-5892 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-BQ-7056         TCGA-IA-A83W         TCGA-Y8-A8RZ 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-2Z-A9J1         TCGA-2Z-A9JO         TCGA-4A-A93W 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-4A-A93X         TCGA-4A-A93Y         TCGA-A4-7583 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7915         TCGA-A4-A57E 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-A4-A7UZ         TCGA-AL-3466         TCGA-AL-3472 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B9-7268 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5882         TCGA-BQ-5885 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5889         TCGA-BQ-5890 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5893         TCGA-BQ-5894 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-BQ-7051         TCGA-DW-7963         TCGA-DZ-6131 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-6846         TCGA-GL-7966 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A9DC         TCGA-IA-A40U 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-6720         TCGA-J7-8537 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-J7-A8I2         TCGA-KV-A74V         TCGA-P4-A5E6 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-P4-AAVL         TCGA-SX-A71R 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SP         TCGA-SX-A7SS 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-UN-AAZ9         TCGA-UZ-A9PM         TCGA-UZ-A9PX 
"KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" "KRTAP4-5 WILD-TYPE" 
        TCGA-Y8-A897 
"KRTAP4-5 WILD-TYPE" 
D15V6, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    2  0
  KRTAP4-5 WILD-TYPE 92  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      2    0
  KRTAP4-5 WILD-TYPE   92    9
   clus
vv  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  0                2                 92
  1                0                  9
[1] 2 2
[1] FALSE
D15V7, binary
                    cls
clus                   0   1
  KRTAP4-5 MUTATED     0   5
  KRTAP4-5 WILD-TYPE  76 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      0    5
  KRTAP4-5 WILD-TYPE   76  201
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  FEMALE                0                 76
  MALE                  5                201
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP4-5 MUTATED                                  0     0
  KRTAP4-5 WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KRTAP4-5 MUTATED                           3     2
  KRTAP4-5 WILD-TYPE                        56   198
D15V11, multiclass
                                  clus
vv                                 KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       3                 56
  WHITE                                           2                198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                    cls
clus                   0   1
  KRTAP4-5 MUTATED     0   5
  KRTAP4-5 WILD-TYPE  11 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      0    5
  KRTAP4-5 WILD-TYPE   11  230
                        clus
vv                       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                5                230
[1] 2 2
[1] FALSE

Clustering(16) Variable = BRAF MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  BRAF MUTATED     4   0
  BRAF WILD-TYPE 234  41
  BRAF MUTATED BRAF WILD-TYPE 
             4            275 
  BRAF MUTATED BRAF WILD-TYPE 
             0             41 
$`BRAF MUTATED`
TCGA-AL-3467 TCGA-B1-5398 TCGA-UZ-A9PP TCGA-WN-A9G9 
       70.19        41.13        98.96        26.01 

$`BRAF WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      103.63       125.29        37.35        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 
       65.13       110.73        51.35        31.73        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  BRAF MUTATED BRAF WILD-TYPE 
         26.01           0.10 
  BRAF MUTATED BRAF WILD-TYPE 
         98.96         194.79 
  BRAF MUTATED BRAF WILD-TYPE 
         55.66          24.89 
[1] "26.0 - 99.0 (55.7)" "0.1 - 194.8 (24.9)"
[1] "hr="     "2.5e+07"
D16V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  BRAF MUTATED         2        0         1        0
  BRAF WILD-TYPE     168       21        48       15
D16V3, multiclass
           clus
vv          BRAF MUTATED BRAF WILD-TYPE
  STAGE I              2            168
  STAGE II             0             21
  STAGE III            1             48
  STAGE IV             0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  BRAF MUTATED     3   0     1
  BRAF WILD-TYPE 186  32    58
D16V4, multiclass
       clus
vv      BRAF MUTATED BRAF WILD-TYPE
  T1               3            186
  T2               0             32
  T3+T4            1             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  BRAF MUTATED    1     0
  BRAF WILD-TYPE 48    25
D16V5, multiclass
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             1             73 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-2Z-A9J1     TCGA-2Z-A9JO     TCGA-4A-A93W 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7583     TCGA-A4-7585 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A7UZ     TCGA-AL-3466 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-A655 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B1-A656     TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-DW-7963     TCGA-DZ-6131 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-F9-A8NY     TCGA-F9-A97G     TCGA-G7-6789     TCGA-G7-6793 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LD     TCGA-GL-6846 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-GL-7966     TCGA-GL-A59R     TCGA-GL-A9DC     TCGA-IA-A40U 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KV-A74V     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-P4-AAVL     TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Y8-A897 
"BRAF WILD-TYPE" 
D16V6, binary
                cls
clus              0  1
  BRAF MUTATED    2  0
  BRAF WILD-TYPE 92  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      2    0
  BRAF WILD-TYPE   92    9
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0            2             92
  1            0              9
[1] 2 2
[1] FALSE
D16V7, binary
                cls
clus               0   1
  BRAF MUTATED     1   3
  BRAF WILD-TYPE  75 203
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1    3
  BRAF WILD-TYPE   75  203
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE            1             75
  MALE              3            203
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             1             75 
    TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU     TCGA-B9-A44B 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838     TCGA-GL-A59T 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU     TCGA-SX-A71W 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ     TCGA-2Z-A9J2 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-2Z-A9J5     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-2Z-A9JK     TCGA-2Z-A9JM     TCGA-2Z-A9JN     TCGA-2Z-A9JO 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-5P-A9K3     TCGA-5P-A9KE 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4117     TCGA-B9-7268 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6792 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LB 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-IA-A83S     TCGA-IA-A83V     TCGA-MH-A854     TCGA-MH-A856 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-Q2-A5QZ     TCGA-SX-A71S 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SR 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Y8-A894     TCGA-Y8-A896     TCGA-Y8-A8RY 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
D16V10, continuous
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             1             54 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-2Z-A9J3     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6793 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-IA-A40U     TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E6 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-UZ-A9PS     TCGA-UZ-A9PX     TCGA-WN-AB4C     TCGA-Y8-A894 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRAF MUTATED                                  0     0
  BRAF WILD-TYPE                                2     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED                           0     4
  BRAF WILD-TYPE                        59   196
D16V11, multiclass
                                  clus
vv                                 BRAF MUTATED BRAF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              6
  BLACK OR AFRICAN AMERICAN                   0             59
  WHITE                                       4            196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                cls
clus               0   1
  BRAF MUTATED     0   4
  BRAF WILD-TYPE  11 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      0    4
  BRAF WILD-TYPE   11  231
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            4            231
[1] 2 2
[1] FALSE

Clustering(17) Variable = KIAA0922 MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                  0   1
  KIAA0922 MUTATED     4   1
  KIAA0922 WILD-TYPE 234  40
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 5                274 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 1                 40 
$`KIAA0922 MUTATED`
TCGA-2Z-A9JS TCGA-Y8-A898 TCGA-2Z-A9JE TCGA-B1-A656 TCGA-DZ-6132 
       16.18        15.62        56.81        20.32        80.88 

$`KIAA0922 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JT TCGA-5P-A9JU 
       34.85        39.88        33.07        25.58        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU 
       16.34        12.13        29.26        19.73        17.75        12.49 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       35.38        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
       56.91         4.57        91.73        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       16.77        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
             15.62               0.10 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
             80.88             194.79 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
            20.320             25.235 
[1] "15.6 - 80.9 (20.3)" "0.1 - 194.8 (25.2)"
[1] "hr=" "1.2"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA0922 MUTATED         5        0         0        0
  KIAA0922 WILD-TYPE     165       21        49       15
D17V3, multiclass
           clus
vv          KIAA0922 MUTATED KIAA0922 WILD-TYPE
  STAGE I                  5                165
  STAGE II                 0                 21
  STAGE III                0                 49
  STAGE IV                 0                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  KIAA0922 MUTATED     5   0     0
  KIAA0922 WILD-TYPE 184  32    59
D17V4, multiclass
       clus
vv      KIAA0922 MUTATED KIAA0922 WILD-TYPE
  T1                   5                184
  T2                   0                 32
  T3+T4                0                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  KIAA0922 MUTATED    1     0
  KIAA0922 WILD-TYPE 48    25
D17V5, multiclass
[1] "Remove cluster labels:" "KIAA0922 MUTATED"      
clus
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 1                 73 
        TCGA-5P-A9JU         TCGA-A4-A5Y1         TCGA-B1-A47O 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B1-A657         TCGA-BQ-5888         TCGA-BQ-5892 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7056         TCGA-IA-A83W         TCGA-Y8-A8RZ 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9J1         TCGA-2Z-A9JO         TCGA-4A-A93W 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-4A-A93X         TCGA-4A-A93Y         TCGA-A4-7583 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7915         TCGA-A4-A57E 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-A7UZ         TCGA-AL-3466         TCGA-AL-3472 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B1-A655         TCGA-B9-7268         TCGA-BQ-5877 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5885         TCGA-BQ-5887 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7963         TCGA-DZ-6131         TCGA-F9-A8NY 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6789         TCGA-G7-6793 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-G7-A8LD 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-GL-A59R 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-GL-A9DC         TCGA-IA-A40U         TCGA-IA-A40Y 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-J7-A8I2 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KV-A74V         TCGA-P4-A5E6         TCGA-P4-A5E8 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-P4-AAVL         TCGA-SX-A71R 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SP         TCGA-SX-A7SS 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UN-AAZ9         TCGA-UZ-A9PM         TCGA-UZ-A9PX 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-Y8-A897 
"KIAA0922 WILD-TYPE" 
D17V6, binary
                    cls
clus                  0  1
  KIAA0922 MUTATED    1  0
  KIAA0922 WILD-TYPE 93  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED      1    0
  KIAA0922 WILD-TYPE   93    9
   clus
vv  KIAA0922 MUTATED KIAA0922 WILD-TYPE
  0                1                 93
  1                0                  9
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                   0   1
  KIAA0922 MUTATED     0   5
  KIAA0922 WILD-TYPE  76 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED      0    5
  KIAA0922 WILD-TYPE   76  201
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  FEMALE                0                 76
  MALE                  5                201
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "KIAA0922 MUTATED"      
clus
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 1                 75 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A71W         TCGA-SX-A7SO 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PZ         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8098 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-7963         TCGA-EV-5901 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-F9-A7Q0 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LC 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-IA-A40U 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SP 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SU         TCGA-UZ-A9PL         TCGA-V9-A7HT 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
D17V9, continuous
D17V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0922 MUTATED                                  0     0
  KIAA0922 WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0922 MUTATED                           0     4
  KIAA0922 WILD-TYPE                        59   196
D17V11, multiclass
                                  clus
vv                                 KIAA0922 MUTATED KIAA0922 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 59
  WHITE                                           4                196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                    cls
clus                   0   1
  KIAA0922 MUTATED     0   4
  KIAA0922 WILD-TYPE  11 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED      0    4
  KIAA0922 WILD-TYPE   11  231
                        clus
vv                       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                4                231
[1] 2 2
[1] FALSE

Clustering(18) Variable = KRT2 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  KRT2 MUTATED     5   0
  KRT2 WILD-TYPE 233  41
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            274 
  KRT2 MUTATED KRT2 WILD-TYPE 
             0             41 
$`KRT2 MUTATED`
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-F9-A97G TCGA-HE-A5NI TCGA-P4-A5E7 
       34.85        56.81         0.43        11.84        87.09 

$`KRT2 WILD-TYPE`
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU 
       16.34        12.13        29.26        19.73        17.75        12.49 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       35.38        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
      100.27        56.91         4.57        91.73        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       58.19        26.01        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 
       20.25        17.62        31.13        15.48        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  KRT2 MUTATED KRT2 WILD-TYPE 
          0.43           0.10 
  KRT2 MUTATED KRT2 WILD-TYPE 
         87.09         194.79 
  KRT2 MUTATED KRT2 WILD-TYPE 
        34.850         25.185 
[1] "0.4 - 87.1 (34.9)"  "0.1 - 194.8 (25.2)"
[1] "hr="     "9200000"
D18V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  KRT2 MUTATED         4        0         1        0
  KRT2 WILD-TYPE     166       21        48       15
D18V3, multiclass
           clus
vv          KRT2 MUTATED KRT2 WILD-TYPE
  STAGE I              4            166
  STAGE II             0             21
  STAGE III            1             48
  STAGE IV             0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  KRT2 MUTATED     4   0     1
  KRT2 WILD-TYPE 185  32    58
D18V4, multiclass
       clus
vv      KRT2 MUTATED KRT2 WILD-TYPE
  T1               4            185
  T2               0             32
  T3+T4            1             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  KRT2 MUTATED    1     0
  KRT2 WILD-TYPE 48    25
D18V5, multiclass
[1] "Remove cluster labels:" "KRT2 MUTATED"          
clus
  KRT2 MUTATED KRT2 WILD-TYPE 
             1             73 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-2Z-A9J1     TCGA-2Z-A9JO     TCGA-4A-A93W 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7583     TCGA-A4-7585 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A7UZ     TCGA-AL-3466 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-B1-A655     TCGA-B1-A656     TCGA-B9-7268     TCGA-BQ-5877 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5889     TCGA-BQ-5890 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-DW-7963 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-DZ-6131     TCGA-F9-A8NY     TCGA-G7-6789     TCGA-G7-6793 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LD     TCGA-GL-6846 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-GL-7966     TCGA-GL-A59R     TCGA-GL-A9DC     TCGA-IA-A40U 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-KV-A74V     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-P4-AAVL     TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-Y8-A897 
"KRT2 WILD-TYPE" 
D18V6, binary
                cls
clus              0  1
  KRT2 MUTATED    2  0
  KRT2 WILD-TYPE 92  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      2    0
  KRT2 WILD-TYPE   92    9
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0            2             92
  1            0              9
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus               0   1
  KRT2 MUTATED     1   4
  KRT2 WILD-TYPE  75 202
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      1    4
  KRT2 WILD-TYPE   75  202
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  FEMALE            1             75
  MALE              4            202
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "KRT2 MUTATED"          
clus
  KRT2 MUTATED KRT2 WILD-TYPE 
             1             75 
    TCGA-2Z-A9JL     TCGA-2Z-A9JT     TCGA-5P-A9JU     TCGA-DW-5560 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7836     TCGA-DW-7837 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-DW-7842     TCGA-SX-A71W     TCGA-SX-A7SO     TCGA-UZ-A9PZ 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-2Z-A9JK     TCGA-2Z-A9JN     TCGA-4A-A93W     TCGA-4A-A93X 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-4A-A93Y     TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8517 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A48D     TCGA-A4-A4ZT 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-EV-5903     TCGA-F9-A7Q0     TCGA-G7-6789     TCGA-G7-6790 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-G7-A8LB     TCGA-G7-A8LC     TCGA-G7-A8LD     TCGA-G7-A8LE 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71R     TCGA-SX-A71S     TCGA-SX-A71U 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-SX-A71V     TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SN 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-SX-A7SP     TCGA-SX-A7SQ     TCGA-SX-A7SR     TCGA-SX-A7SS 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
    TCGA-SX-A7SU     TCGA-UZ-A9PL     TCGA-V9-A7HT 
"KRT2 WILD-TYPE" "KRT2 WILD-TYPE" "KRT2 WILD-TYPE" 
D18V9, continuous
D18V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT2 MUTATED                                  0     1
  KRT2 WILD-TYPE                                2     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRT2 MUTATED                           0     3
  KRT2 WILD-TYPE                        59   197
D18V11, multiclass
                                  clus
vv                                 KRT2 MUTATED KRT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              5
  BLACK OR AFRICAN AMERICAN                   0             59
  WHITE                                       3            197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                cls
clus               0   1
  KRT2 MUTATED     0   4
  KRT2 WILD-TYPE  11 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      0    4
  KRT2 WILD-TYPE   11  231
                        clus
vv                       KRT2 MUTATED KRT2 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            4            231
[1] 2 2
[1] FALSE

Clustering(19) Variable = ALMS1 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  ALMS1 MUTATED     7   1
  ALMS1 WILD-TYPE 231  40
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              8             271 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              1              40 
$`ALMS1 MUTATED`
TCGA-5P-A9JV TCGA-GL-A9DE TCGA-HE-A5NJ TCGA-J7-A8I2 TCGA-P4-AAVM TCGA-UZ-A9PL 
       67.17        16.31        56.75        10.09        50.60       103.63 
TCGA-UZ-A9PU TCGA-Y8-A896 
       30.67        18.64 

$`ALMS1 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       12.26        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU 
       16.34        12.13        29.26        19.73        17.75        12.49 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       35.38        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL 
       81.93        58.19        26.01        11.84        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-Q2-A5QZ 
       42.94         6.61        99.12        92.58        16.01        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       18.02        26.20       117.40       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       71.24        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       26.01        39.06        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  ALMS1 MUTATED ALMS1 WILD-TYPE 
          10.09            0.10 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
         103.63          194.79 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
         40.635          25.150 
[1] "10.1 - 103.6 (40.6)" "0.1 - 194.8 (25.1)" 
[1] "hr=" "1.6"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ALMS1 MUTATED         4        1         1        0
  ALMS1 WILD-TYPE     166       20        48       15
D19V3, multiclass
           clus
vv          ALMS1 MUTATED ALMS1 WILD-TYPE
  STAGE I               4             166
  STAGE II              1              20
  STAGE III             1              48
  STAGE IV              0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ALMS1 MUTATED     6   1     1
  ALMS1 WILD-TYPE 183  31    58
D19V4, multiclass
       clus
vv      ALMS1 MUTATED ALMS1 WILD-TYPE
  T1                6             183
  T2                1              31
  T3+T4             1              58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  ALMS1 MUTATED    1     0
  ALMS1 WILD-TYPE 48    25
D19V5, multiclass
[1] "Remove cluster labels:" "ALMS1 MUTATED"         
clus
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              1              73 
     TCGA-5P-A9JU      TCGA-A4-A5Y1      TCGA-B1-A47O      TCGA-B1-A657 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5892      TCGA-BQ-7056      TCGA-IA-A83W 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-Y8-A8RZ      TCGA-2Z-A9J1      TCGA-2Z-A9JO      TCGA-4A-A93W 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7583      TCGA-A4-7585 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-7915      TCGA-A4-A57E      TCGA-A4-A7UZ      TCGA-AL-3466 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B1-A655      TCGA-B1-A656      TCGA-B9-7268      TCGA-BQ-5877 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-BQ-5885      TCGA-BQ-5887      TCGA-BQ-5889      TCGA-BQ-5890 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-BQ-5891      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-DW-7963 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DZ-6131      TCGA-F9-A8NY      TCGA-F9-A97G      TCGA-G7-6789 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LD 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-GL-6846      TCGA-GL-7966      TCGA-GL-A59R      TCGA-GL-A9DC 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720      TCGA-J7-8537 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-KV-A74V      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-P4-AAVL      TCGA-SX-A71R      TCGA-SX-A7SM      TCGA-SX-A7SP 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-UN-AAZ9      TCGA-UZ-A9PM      TCGA-UZ-A9PX 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-Y8-A897 
"ALMS1 WILD-TYPE" 
D19V6, binary
                 cls
clus               0  1
  ALMS1 MUTATED    2  0
  ALMS1 WILD-TYPE 92  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED      2    0
  ALMS1 WILD-TYPE   92    9
   clus
vv  ALMS1 MUTATED ALMS1 WILD-TYPE
  0             2              92
  1             0               9
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  ALMS1 MUTATED     0   8
  ALMS1 WILD-TYPE  76 198
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED      0    8
  ALMS1 WILD-TYPE   76  198
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  FEMALE             0              76
  MALE               8             198
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "ALMS1 MUTATED"         
clus
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              1              75 
     TCGA-2Z-A9JL      TCGA-2Z-A9JT      TCGA-5P-A9JU      TCGA-DW-5560 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7836      TCGA-DW-7837 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DW-7842      TCGA-SX-A71W      TCGA-SX-A7SO      TCGA-UZ-A9PZ 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9JE      TCGA-2Z-A9JK      TCGA-2Z-A9JN      TCGA-4A-A93W 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7286      TCGA-A4-7828 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A48D 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963      TCGA-EV-5901 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A7Q0      TCGA-G7-6789 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-G7-A8LB      TCGA-G7-A8LC      TCGA-G7-A8LD 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-A8LE      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ      TCGA-SX-A71R      TCGA-SX-A71S 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A71U      TCGA-SX-A71V      TCGA-SX-A7SL      TCGA-SX-A7SM 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ      TCGA-SX-A7SR 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-V9-A7HT 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
D19V9, continuous
[1] "Remove cluster labels:" "ALMS1 MUTATED"         
clus
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              2              74 
     TCGA-2Z-A9JD      TCGA-2Z-A9JQ      TCGA-5P-A9JU      TCGA-B9-A44B 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838      TCGA-GL-A59T 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-IZ-A6M8      TCGA-PJ-A5Z9      TCGA-PJ-A8JU      TCGA-SX-A71W 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ      TCGA-2Z-A9J2 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9J5      TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9JK      TCGA-2Z-A9JM      TCGA-2Z-A9JN      TCGA-2Z-A9JO 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-4A-A93W      TCGA-4A-A93Y      TCGA-5P-A9K3      TCGA-5P-A9KE 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173      TCGA-B1-A654 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4117      TCGA-B9-7268 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6792 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LB 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-GL-7773      TCGA-GL-A9DD 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-HE-A5NK      TCGA-IA-A40U      TCGA-IA-A83S 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-IA-A83V      TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E7 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-P4-A5EB      TCGA-Q2-A5QZ      TCGA-SX-A71S      TCGA-SX-A71U 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SL      TCGA-SX-A7SM      TCGA-SX-A7SR      TCGA-SX-A7SS 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-UZ-A9PM      TCGA-UZ-A9PS      TCGA-UZ-A9PX      TCGA-WN-A9G9 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-Y8-A894      TCGA-Y8-A8RY 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
D19V10, continuous
[1] "Remove cluster labels:" "ALMS1 MUTATED"         
clus
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              1              54 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9J3      TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-A8LE      TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-Q2-A5QZ      TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SM      TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-UZ-A9PS      TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-WN-AB4C 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-Y8-A894      TCGA-Y8-A8RY 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALMS1 MUTATED                                  0     1
  ALMS1 WILD-TYPE                                2     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALMS1 MUTATED                           1     5
  ALMS1 WILD-TYPE                        58   195
D19V11, multiclass
                                  clus
vv                                 ALMS1 MUTATED ALMS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               5
  BLACK OR AFRICAN AMERICAN                    1              58
  WHITE                                        5             195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                 cls
clus                0   1
  ALMS1 MUTATED     1   6
  ALMS1 WILD-TYPE  10 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED      1    6
  ALMS1 WILD-TYPE   10  229
                        clus
vv                       ALMS1 MUTATED ALMS1 WILD-TYPE
  HISPANIC OR LATINO                 1              10
  NOT HISPANIC OR LATINO             6             229
[1] 2 2
[1] FALSE

Clustering(20) Variable = GXYLT1 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  GXYLT1 MUTATED     4   0
  GXYLT1 WILD-TYPE 234  41
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               4              275 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               0               41 
$`GXYLT1 MUTATED`
TCGA-2Z-A9JD TCGA-A4-A5DU TCGA-B9-A5W9 TCGA-Y8-A8RY 
       34.85        16.31         0.16        25.28 

$`GXYLT1 WILD-TYPE`
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU 
       16.34        12.13        29.26        19.73        17.75        12.49 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       35.38        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E 
        0.46         1.15        43.99        22.06        17.23        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05         6.02        13.28 

  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
            0.16             0.10 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
           34.85           194.79 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
          20.795           25.220 
[1] "0.2 - 34.9 (20.8)"  "0.1 - 194.8 (25.2)"
[1] "hr="     "3300000"
D20V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GXYLT1 MUTATED         4        0         0        0
  GXYLT1 WILD-TYPE     166       21        49       15
D20V3, multiclass
           clus
vv          GXYLT1 MUTATED GXYLT1 WILD-TYPE
  STAGE I                4              166
  STAGE II               0               21
  STAGE III              0               49
  STAGE IV               0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  GXYLT1 MUTATED     4   0     0
  GXYLT1 WILD-TYPE 185  32    59
D20V4, multiclass
       clus
vv      GXYLT1 MUTATED GXYLT1 WILD-TYPE
  T1                 4              185
  T2                 0               32
  T3+T4              0               59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  GXYLT1 MUTATED    0     0
  GXYLT1 WILD-TYPE 49    25
D20V5, multiclass
D20V6, binary
                  cls
clus                0  1
  GXYLT1 MUTATED    0  0
  GXYLT1 WILD-TYPE 94  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED      0    0
  GXYLT1 WILD-TYPE   94    9
D20V7, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED     1   3
  GXYLT1 WILD-TYPE  75 203
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED      1    3
  GXYLT1 WILD-TYPE   75  203
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  FEMALE              1               75
  MALE                3              203
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "GXYLT1 MUTATED"        
clus
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               1               75 
      TCGA-2Z-A9JL       TCGA-2Z-A9JT       TCGA-5P-A9JU       TCGA-DW-5560 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7836       TCGA-DW-7837 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-DW-7842       TCGA-SX-A71W       TCGA-SX-A7SO       TCGA-UZ-A9PZ 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN       TCGA-4A-A93W 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286       TCGA-A4-7828 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-EV-5903       TCGA-F9-A7Q0       TCGA-G7-6789       TCGA-G7-6790 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-6796 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LC       TCGA-G7-A8LD       TCGA-G7-A8LE 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-Q2-A5QZ       TCGA-SX-A71R       TCGA-SX-A71S       TCGA-SX-A71U 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-SX-A71V       TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SN 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR       TCGA-SX-A7SS 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
D20V9, continuous
[1] "Remove cluster labels:" "GXYLT1 MUTATED"        
clus
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               2               74 
      TCGA-2Z-A9JQ       TCGA-5P-A9JU       TCGA-B9-A44B       TCGA-DW-5561 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-DW-7834       TCGA-DW-7838       TCGA-GL-A59T       TCGA-IZ-A6M8 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-PJ-A5Z9       TCGA-PJ-A8JU       TCGA-SX-A71W       TCGA-UZ-A9PO 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-UZ-A9PR       TCGA-Y8-A8RZ       TCGA-2Z-A9J2       TCGA-2Z-A9J5 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JK 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-2Z-A9JM       TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93W 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-4A-A93Y       TCGA-5P-A9K3       TCGA-5P-A9KE       TCGA-A4-8310 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-AL-3472       TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-B9-4115       TCGA-B9-4117       TCGA-B9-7268       TCGA-B9-A69E 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-DW-7963       TCGA-F9-A97G       TCGA-G7-6792       TCGA-G7-6793 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-G7-A8LE       TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U       TCGA-IA-A83S 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-IA-A83V       TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E7 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-P4-A5EB       TCGA-Q2-A5QZ       TCGA-SX-A71S       TCGA-SX-A71U 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SR       TCGA-SX-A7SS 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-UZ-A9PM       TCGA-UZ-A9PS       TCGA-UZ-A9PX       TCGA-WN-A9G9 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-Y8-A894       TCGA-Y8-A896 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
D20V10, continuous
[1] "Remove cluster labels:" "GXYLT1 MUTATED"        
clus
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               2               53 
      TCGA-DW-5561       TCGA-PJ-A5Z9       TCGA-PJ-A8JU       TCGA-SX-A71W 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ       TCGA-2Z-A9J3 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JN 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-A4-A48D 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472       TCGA-AL-7173 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117       TCGA-B9-A69E 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-DW-7963       TCGA-F9-A97G       TCGA-G7-6793       TCGA-G7-6795 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-IA-A40U 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E6       TCGA-Q2-A5QZ 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-WN-AB4C       TCGA-Y8-A894 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-Y8-A896 
"GXYLT1 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GXYLT1 MUTATED                                  0     0
  GXYLT1 WILD-TYPE                                2     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GXYLT1 MUTATED                           0     4
  GXYLT1 WILD-TYPE                        59   196
D20V11, multiclass
                                  clus
vv                                 GXYLT1 MUTATED GXYLT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                6
  BLACK OR AFRICAN AMERICAN                     0               59
  WHITE                                         4              196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED     0   4
  GXYLT1 WILD-TYPE  11 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED      0    4
  GXYLT1 WILD-TYPE   11  231
                        clus
vv                       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              4              231
[1] 2 2
[1] FALSE

Clustering(21) Variable = ATP1B1 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2                0   1
  ATP1B1 MUTATED     6   1
  ATP1B1 WILD-TYPE 232  40
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
               7              272 
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
               1               40 
$`ATP1B1 MUTATED`
TCGA-A4-8098 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-4103 TCGA-BQ-7050 TCGA-F9-A4JJ 
       29.46        41.13        37.51        30.58        61.28        10.68 
TCGA-WN-AB4C 
       39.06 

$`ATP1B1 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A654 
       66.71        62.66        67.73         2.20        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       16.77        20.32        33.83        29.03        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
      123.62        48.26        93.34        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 
       51.19        74.60        34.19        19.00        24.89        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        26.01        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
           10.68             0.10 
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
           61.28           194.79 
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
          37.510           24.675 
[1] "10.7 - 61.3 (37.5)" "0.1 - 194.8 (24.7)"
[1] "hr=" "1"  
D21V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ATP1B1 MUTATED         4        1         2        0
  ATP1B1 WILD-TYPE     166       20        47       15
D21V3, multiclass
           clus
vv          ATP1B1 MUTATED ATP1B1 WILD-TYPE
  STAGE I                4              166
  STAGE II               1               20
  STAGE III              2               47
  STAGE IV               0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ATP1B1 MUTATED     4   1     2
  ATP1B1 WILD-TYPE 185  31    57
D21V4, multiclass
       clus
vv      ATP1B1 MUTATED ATP1B1 WILD-TYPE
  T1                 4              185
  T2                 1               31
  T3+T4              2               57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  ATP1B1 MUTATED    2     0
  ATP1B1 WILD-TYPE 47    25
D21V5, multiclass
[1] "Remove cluster labels:" "ATP1B1 MUTATED"        
clus
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
               2               72 
      TCGA-5P-A9JU       TCGA-A4-A5Y1       TCGA-B1-A47O       TCGA-B1-A657 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5892       TCGA-BQ-7056       TCGA-IA-A83W 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-Y8-A8RZ       TCGA-2Z-A9J1       TCGA-2Z-A9JO       TCGA-4A-A93W 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7583       TCGA-A4-7585 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-A4-7915       TCGA-A4-A57E       TCGA-A4-A7UZ       TCGA-AL-3466 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173       TCGA-B1-A655 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-B1-A656       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-BQ-7051       TCGA-DW-7963       TCGA-DZ-6131       TCGA-F9-A8NY 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-F9-A97G       TCGA-G7-6789       TCGA-G7-6793       TCGA-G7-6795 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-A8LD       TCGA-GL-6846       TCGA-GL-7966 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-GL-A59R       TCGA-GL-A9DC       TCGA-IA-A40U       TCGA-IA-A40Y 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-J7-6720       TCGA-J7-8537       TCGA-J7-A8I2       TCGA-KV-A74V 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA       TCGA-P4-AAVL 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-SX-A71R       TCGA-SX-A7SM       TCGA-SX-A7SP       TCGA-SX-A7SS 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-UN-AAZ9       TCGA-UZ-A9PM       TCGA-UZ-A9PX       TCGA-Y8-A897 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
D21V6, binary
                  cls
clus                0  1
  ATP1B1 MUTATED    3  0
  ATP1B1 WILD-TYPE 91  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1B1 MUTATED      3    0
  ATP1B1 WILD-TYPE   91    9
   clus
vv  ATP1B1 MUTATED ATP1B1 WILD-TYPE
  0              3               91
  1              0                9
[1] 2 2
[1] FALSE
D21V7, binary
                  cls
clus                 0   1
  ATP1B1 MUTATED     4   3
  ATP1B1 WILD-TYPE  72 203
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1B1 MUTATED      4    3
  ATP1B1 WILD-TYPE   72  203
        clus
vv       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  FEMALE              4               72
  MALE                3              203
[1] 2 2
[1] FALSE
D21V8, continuous
[1] "Remove cluster labels:" "ATP1B1 MUTATED"        
clus
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
               1               75 
      TCGA-2Z-A9JL       TCGA-2Z-A9JT       TCGA-5P-A9JU       TCGA-DW-5560 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7836       TCGA-DW-7837 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-DW-7842       TCGA-SX-A71W       TCGA-SX-A7SO       TCGA-UZ-A9PZ 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN       TCGA-4A-A93W 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286       TCGA-A4-7828 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-EV-5903       TCGA-F9-A7Q0       TCGA-G7-6789       TCGA-G7-6790 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-6796 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LC       TCGA-G7-A8LD       TCGA-G7-A8LE 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-Q2-A5QZ       TCGA-SX-A71R       TCGA-SX-A71S       TCGA-SX-A71U 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-SX-A71V       TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SN 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR       TCGA-SX-A7SS 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
D21V9, continuous
D21V10, continuous
[1] "Remove cluster labels:" "ATP1B1 MUTATED"        
clus
  ATP1B1 MUTATED ATP1B1 WILD-TYPE 
               1               54 
      TCGA-2Z-A9JD       TCGA-DW-5561       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-2Z-A9J3       TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-B9-A69E       TCGA-DW-7963       TCGA-F9-A97G       TCGA-G7-6793 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-G7-A8LE       TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E6 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-Q2-A5QZ       TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-SX-A7SM       TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-UZ-A9PS       TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-Y8-A894 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
      TCGA-Y8-A896       TCGA-Y8-A8RY 
"ATP1B1 WILD-TYPE" "ATP1B1 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP1B1 MUTATED                                  0     0
  ATP1B1 WILD-TYPE                                2     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP1B1 MUTATED                           3     4
  ATP1B1 WILD-TYPE                        56   196
D21V11, multiclass
                                  clus
vv                                 ATP1B1 MUTATED ATP1B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                6
  BLACK OR AFRICAN AMERICAN                     3               56
  WHITE                                         4              196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                  cls
clus                 0   1
  ATP1B1 MUTATED     1   5
  ATP1B1 WILD-TYPE  10 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1B1 MUTATED      1    5
  ATP1B1 WILD-TYPE   10  230
                        clus
vv                       ATP1B1 MUTATED ATP1B1 WILD-TYPE
  HISPANIC OR LATINO                  1               10
  NOT HISPANIC OR LATINO              5              230
[1] 2 2
[1] FALSE

Clustering(22) Variable = PBRM1 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED     7   4
  PBRM1 WILD-TYPE 231  37
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             11             268 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              4              37 
$`PBRM1 MUTATED`
TCGA-5P-A9JU TCGA-B9-A44B TCGA-BQ-7058 TCGA-IA-A83W TCGA-4A-A93X TCGA-5P-A9K3 
       12.26        11.87        11.28        67.17        12.82        15.48 
TCGA-A4-7583 TCGA-BQ-5890 TCGA-BQ-7061 TCGA-GL-A9DE TCGA-UZ-A9PJ 
        0.10         7.66         7.17        16.31        26.20 

$`PBRM1 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       26.27        20.12        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       61.02        17.95        84.89        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE 
       86.37        21.60        15.91        15.62         6.74         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 
      106.55        49.58        90.21        22.26        78.64        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       19.63        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 
       40.83        26.04        30.28        25.35        10.82         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 
       50.40        49.84         7.63         7.04         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 
        1.05        12.43        12.89        11.21        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        18.02       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.10            0.13 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          67.17          194.79 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         12.260          25.465 
[1] "0.1 - 67.2 (12.3)"  "0.1 - 194.8 (25.5)"
[1] "hr=" "5.7"
D22V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PBRM1 MUTATED         5        0         4        1
  PBRM1 WILD-TYPE     165       21        45       14
D22V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I               5             165
  STAGE II              0              21
  STAGE III             4              45
  STAGE IV              1              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PBRM1 MUTATED     5   1     5
  PBRM1 WILD-TYPE 184  31    54
D22V4, multiclass
       clus
vv      PBRM1 MUTATED PBRM1 WILD-TYPE
  T1                5             184
  T2                1              31
  T3+T4             5              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  PBRM1 MUTATED    4     1
  PBRM1 WILD-TYPE 45    24
D22V5, multiclass
       clus
vv      PBRM1 MUTATED PBRM1 WILD-TYPE
  N0                4              45
  N1+N2             1              24
[1] 2 2
[1] FALSE
D22V6, binary
                 cls
clus               0  1
  PBRM1 MUTATED    6  0
  PBRM1 WILD-TYPE 88  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      6    0
  PBRM1 WILD-TYPE   88    9
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             6              88
  1             0               9
[1] 2 2
[1] FALSE
D22V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED     1  10
  PBRM1 WILD-TYPE  75 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      1   10
  PBRM1 WILD-TYPE   75  196
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE             1              75
  MALE              10             196
[1] 2 2
[1] FALSE
D22V8, continuous
[1] "Remove cluster labels:" "PBRM1 MUTATED"         
clus
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              2              74 
     TCGA-2Z-A9JL      TCGA-2Z-A9JT      TCGA-DW-5560      TCGA-DW-5561 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7836      TCGA-DW-7837      TCGA-DW-7838 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-SX-A7SO      TCGA-UZ-A9PZ      TCGA-2Z-A9JE 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-2Z-A9JK      TCGA-2Z-A9JN      TCGA-4A-A93W      TCGA-4A-A93Y 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-F9-A7Q0      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM      TCGA-G7-A8LB 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-G7-A8LC      TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-IA-A40U 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-SX-A71R      TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A71V 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-SX-A7SL      TCGA-SX-A7SM      TCGA-SX-A7SN      TCGA-SX-A7SP 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-SX-A7SQ      TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-SX-A7SU 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-UZ-A9PL      TCGA-V9-A7HT 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
D22V9, continuous
D22V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PBRM1 MUTATED                                  0     0
  PBRM1 WILD-TYPE                                2     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED                           3     8
  PBRM1 WILD-TYPE                        56   192
D22V11, multiclass
                                  clus
vv                                 PBRM1 MUTATED PBRM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               6
  BLACK OR AFRICAN AMERICAN                    3              56
  WHITE                                        8             192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                 cls
clus                0   1
  PBRM1 MUTATED     0  11
  PBRM1 WILD-TYPE  11 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      0   11
  PBRM1 WILD-TYPE   11  224
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO            11             224
[1] 2 2
[1] FALSE

Clustering(23) Variable = PTEN MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     7   0
  PTEN WILD-TYPE 231  41
  PTEN MUTATED PTEN WILD-TYPE 
             7            272 
  PTEN MUTATED PTEN WILD-TYPE 
             0             41 
$`PTEN MUTATED`
TCGA-B1-A657 TCGA-PJ-A8JU TCGA-A4-7996 TCGA-BQ-7051 TCGA-P4-A5E7 TCGA-UZ-A9Q1 
       21.07        12.49        16.64        50.40        87.09        51.35 
TCGA-Y8-A897 
       18.05 

$`PTEN WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        49.25        21.67        27.68        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71W 
       16.34        12.13        29.26        19.73        17.75        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7997 TCGA-A4-8098 
       35.18        19.13         7.82         0.23        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 
        2.76       123.62        48.26        93.34        61.28        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 
       20.25        17.62        31.13        15.48        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY 
       31.73        26.01        39.06        18.64        18.64        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  PTEN MUTATED PTEN WILD-TYPE 
         12.49           0.10 
  PTEN MUTATED PTEN WILD-TYPE 
         87.09         194.79 
  PTEN MUTATED PTEN WILD-TYPE 
        21.070         25.235 
[1] "12.5 - 87.1 (21.1)" "0.1 - 194.8 (25.2)"
[1] "hr="     "2.5e+07"
D23V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED         6        1         0        0
  PTEN WILD-TYPE     164       20        49       15
D23V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              6            164
  STAGE II             1             20
  STAGE III            0             49
  STAGE IV             0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  PTEN MUTATED     6   1     0
  PTEN WILD-TYPE 183  31    59
D23V4, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T1               6            183
  T2               1             31
  T3+T4            0             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  PTEN MUTATED    3     0
  PTEN WILD-TYPE 46    25
D23V5, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  N0               3             46
  N1+N2            0             25
[1] 2 2
[1] FALSE
D23V6, binary
                cls
clus              0  1
  PTEN MUTATED    2  0
  PTEN WILD-TYPE 92  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2    0
  PTEN WILD-TYPE   92    9
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            2             92
  1            0              9
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus               0   1
  PTEN MUTATED     5   2
  PTEN WILD-TYPE  71 204
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    2
  PTEN WILD-TYPE   71  204
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            5             71
  MALE              2            204
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2             74 
    TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU     TCGA-B9-A44B 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838     TCGA-GL-A59T 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-SX-A71W     TCGA-UZ-A9PO 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-UZ-A9PR     TCGA-Y8-A8RZ     TCGA-2Z-A9J2     TCGA-2Z-A9J5 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JK 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-2Z-A9JM     TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-4A-A93Y     TCGA-5P-A9K3     TCGA-5P-A9KE     TCGA-A4-8310 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3466 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B9-4115     TCGA-B9-4117     TCGA-B9-7268     TCGA-B9-A69E 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6792     TCGA-G7-6793 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U     TCGA-IA-A83S 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-IA-A83V     TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5EB 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-UZ-A9PS     TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-Y8-A894 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" 
D23V10, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1             54 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-SX-A71W 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ     TCGA-2Z-A9J3 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JN 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-A4-A48D 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472     TCGA-AL-7173 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117     TCGA-B9-A69E 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6793     TCGA-G7-6795 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-IA-A40U 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E6     TCGA-Q2-A5QZ 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     0
  PTEN WILD-TYPE                                2     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           0     7
  PTEN WILD-TYPE                        59   193
D23V11, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              6
  BLACK OR AFRICAN AMERICAN                   0             59
  WHITE                                       7            193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                cls
clus               0   1
  PTEN MUTATED     0   6
  PTEN WILD-TYPE  11 229
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    6
  PTEN WILD-TYPE   11  229
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            6            229
[1] 2 2
[1] FALSE

Clustering(24) Variable = SAV1 MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  SAV1 MUTATED     5   1
  SAV1 WILD-TYPE 233  40
  SAV1 MUTATED SAV1 WILD-TYPE 
             6            273 
  SAV1 MUTATED SAV1 WILD-TYPE 
             1             40 
$`SAV1 MUTATED`
TCGA-2Z-A9JG TCGA-B3-3926 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-A8LC TCGA-HE-A5NK 
       54.64        29.03        13.08         4.01        23.08        73.25 

$`SAV1 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
       36.49        20.25        16.77        20.32        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       19.00        24.89        10.68         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       20.52        25.84        25.25        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       11.84        56.75        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  SAV1 MUTATED SAV1 WILD-TYPE 
          4.01           0.10 
  SAV1 MUTATED SAV1 WILD-TYPE 
         73.25         194.79 
  SAV1 MUTATED SAV1 WILD-TYPE 
        26.055         25.220 
[1] "4.0 - 73.2 (26.1)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "1.2"
D24V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SAV1 MUTATED         4        0         0        1
  SAV1 WILD-TYPE     166       21        49       14
D24V3, multiclass
           clus
vv          SAV1 MUTATED SAV1 WILD-TYPE
  STAGE I              4            166
  STAGE II             0             21
  STAGE III            0             49
  STAGE IV             1             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  SAV1 MUTATED     5   0     1
  SAV1 WILD-TYPE 184  32    58
D24V4, multiclass
       clus
vv      SAV1 MUTATED SAV1 WILD-TYPE
  T1               5            184
  T2               0             32
  T3+T4            1             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  SAV1 MUTATED    0     1
  SAV1 WILD-TYPE 49    24
D24V5, multiclass
[1] "Remove cluster labels:" "SAV1 MUTATED"          
clus
  SAV1 MUTATED SAV1 WILD-TYPE 
             1             73 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-2Z-A9J1     TCGA-2Z-A9JO     TCGA-4A-A93W 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7583     TCGA-A4-7585 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A7UZ     TCGA-AL-3466 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-B1-A655     TCGA-B1-A656     TCGA-B9-7268     TCGA-BQ-5877 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5889     TCGA-BQ-5890 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-DW-7963 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-DZ-6131     TCGA-F9-A8NY     TCGA-F9-A97G     TCGA-G7-6793 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LD     TCGA-GL-6846 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-GL-7966     TCGA-GL-A59R     TCGA-GL-A9DC     TCGA-IA-A40U 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-KV-A74V     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-P4-AAVL     TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-Y8-A897 
"SAV1 WILD-TYPE" 
D24V6, binary
                cls
clus              0  1
  SAV1 MUTATED    3  0
  SAV1 WILD-TYPE 91  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAV1 MUTATED      3    0
  SAV1 WILD-TYPE   91    9
   clus
vv  SAV1 MUTATED SAV1 WILD-TYPE
  0            3             91
  1            0              9
[1] 2 2
[1] FALSE
D24V7, binary
                cls
clus               0   1
  SAV1 MUTATED     3   3
  SAV1 WILD-TYPE  73 203
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAV1 MUTATED      3    3
  SAV1 WILD-TYPE   73  203
        clus
vv       SAV1 MUTATED SAV1 WILD-TYPE
  FEMALE            3             73
  MALE              3            203
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
[1] "Remove cluster labels:" "SAV1 MUTATED"          
clus
  SAV1 MUTATED SAV1 WILD-TYPE 
             1             75 
    TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU     TCGA-B9-A44B 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838     TCGA-GL-A59T 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU     TCGA-SX-A71W 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ     TCGA-2Z-A9J2 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-2Z-A9J5     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-2Z-A9JK     TCGA-2Z-A9JM     TCGA-2Z-A9JN     TCGA-2Z-A9JO 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-5P-A9K3     TCGA-5P-A9KE 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4117     TCGA-B9-7268 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6792 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LB 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-IA-A40U     TCGA-IA-A83S 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-IA-A83V     TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E7 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-P4-A5EB     TCGA-Q2-A5QZ     TCGA-SX-A71S     TCGA-SX-A71U 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SR     TCGA-SX-A7SS 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX     TCGA-WN-A9G9 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
    TCGA-Y8-A894     TCGA-Y8-A896     TCGA-Y8-A8RY 
"SAV1 WILD-TYPE" "SAV1 WILD-TYPE" "SAV1 WILD-TYPE" 
D24V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAV1 MUTATED                                  0     1
  SAV1 WILD-TYPE                                2     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SAV1 MUTATED                           0     4
  SAV1 WILD-TYPE                        59   196
D24V11, multiclass
                                  clus
vv                                 SAV1 MUTATED SAV1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              5
  BLACK OR AFRICAN AMERICAN                   0             59
  WHITE                                       4            196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                cls
clus               0   1
  SAV1 MUTATED     0   5
  SAV1 WILD-TYPE  11 230
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAV1 MUTATED      0    5
  SAV1 WILD-TYPE   11  230
                        clus
vv                       SAV1 MUTATED SAV1 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            5            230
[1] 2 2
[1] FALSE

Clustering(25) Variable = CALCR MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  CALCR MUTATED     1   2
  CALCR WILD-TYPE 237  39
  CALCR MUTATED CALCR WILD-TYPE 
              3             276 
  CALCR MUTATED CALCR WILD-TYPE 
              2              39 
$`CALCR MUTATED`
TCGA-BQ-5889 TCGA-GL-A9DC TCGA-P4-AAVL 
       10.82        12.89        16.01 

$`CALCR WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 
       21.63        40.83        26.04        30.28        25.35         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DD TCGA-GL-A9DE 
        3.68        27.65         1.05        12.43        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  CALCR MUTATED CALCR WILD-TYPE 
          10.82            0.10 
  CALCR MUTATED CALCR WILD-TYPE 
          16.01          194.79 
  CALCR MUTATED CALCR WILD-TYPE 
         12.890          25.265 
[1] "10.8 - 16.0 (12.9)" "0.1 - 194.8 (25.3)"
[1] "hr=" "14" 
D25V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CALCR MUTATED         1        0         1        1
  CALCR WILD-TYPE     169       21        48       14
D25V3, multiclass
           clus
vv          CALCR MUTATED CALCR WILD-TYPE
  STAGE I               1             169
  STAGE II              0              21
  STAGE III             1              48
  STAGE IV              1              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CALCR MUTATED     1   0     2
  CALCR WILD-TYPE 188  32    57
D25V4, multiclass
       clus
vv      CALCR MUTATED CALCR WILD-TYPE
  T1                1             188
  T2                0              32
  T3+T4             2              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  CALCR MUTATED    2     1
  CALCR WILD-TYPE 47    24
D25V5, multiclass
       clus
vv      CALCR MUTATED CALCR WILD-TYPE
  N0                2              47
  N1+N2             1              24
[1] 2 2
[1] FALSE
D25V6, binary
                 cls
clus               0  1
  CALCR MUTATED    0  1
  CALCR WILD-TYPE 94  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALCR MUTATED      0    1
  CALCR WILD-TYPE   94    8
   clus
vv  CALCR MUTATED CALCR WILD-TYPE
  0             0              94
  1             1               8
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus                0   1
  CALCR MUTATED     1   2
  CALCR WILD-TYPE  75 204
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALCR MUTATED      1    2
  CALCR WILD-TYPE   75  204
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  FEMALE             1              75
  MALE               2             204
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CALCR MUTATED                                  0     0
  CALCR WILD-TYPE                                2     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CALCR MUTATED                           0     3
  CALCR WILD-TYPE                        59   197
D25V11, multiclass
                                  clus
vv                                 CALCR MUTATED CALCR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               6
  BLACK OR AFRICAN AMERICAN                    0              59
  WHITE                                        3             197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                 cls
clus                0   1
  CALCR MUTATED     1   2
  CALCR WILD-TYPE  10 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALCR MUTATED      1    2
  CALCR WILD-TYPE   10  233
                        clus
vv                       CALCR MUTATED CALCR WILD-TYPE
  HISPANIC OR LATINO                 1              10
  NOT HISPANIC OR LATINO             2             233
[1] 2 2
[1] FALSE

Clustering(26) Variable = IGSF3 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  IGSF3 MUTATED     3   1
  IGSF3 WILD-TYPE 235  40
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              4             275 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              1              40 
$`IGSF3 MUTATED`
TCGA-SX-A7SO TCGA-BQ-5880 TCGA-GL-A9DE TCGA-MH-A562 
       41.33        43.20        16.31        20.25 

$`IGSF3 WILD-TYPE`
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       12.49        35.38        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 
       27.65         1.05        12.43        12.89        11.21        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.65        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  IGSF3 MUTATED IGSF3 WILD-TYPE 
          16.31            0.10 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
          43.20          194.79 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
          30.79           25.22 
[1] "16.3 - 43.2 (30.8)" "0.1 - 194.8 (25.2)"
[1] "hr=" "2.1"
D26V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  IGSF3 MUTATED         3        0         1        0
  IGSF3 WILD-TYPE     167       21        48       15
D26V3, multiclass
           clus
vv          IGSF3 MUTATED IGSF3 WILD-TYPE
  STAGE I               3             167
  STAGE II              0              21
  STAGE III             1              48
  STAGE IV              0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  IGSF3 MUTATED     3   0     1
  IGSF3 WILD-TYPE 186  32    58
D26V4, multiclass
       clus
vv      IGSF3 MUTATED IGSF3 WILD-TYPE
  T1                3             186
  T2                0              32
  T3+T4             1              58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  IGSF3 MUTATED    0     1
  IGSF3 WILD-TYPE 49    24
D26V5, multiclass
[1] "Remove cluster labels:" "IGSF3 MUTATED"         
clus
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              1              73 
     TCGA-5P-A9JU      TCGA-A4-A5Y1      TCGA-B1-A47O      TCGA-B1-A657 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5892      TCGA-BQ-7056      TCGA-IA-A83W 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-Y8-A8RZ      TCGA-2Z-A9J1      TCGA-2Z-A9JO      TCGA-4A-A93W 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7583      TCGA-A4-7585 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-A4-7915      TCGA-A4-A57E      TCGA-A4-A7UZ      TCGA-AL-3466 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-B1-A655      TCGA-B1-A656      TCGA-B9-7268      TCGA-BQ-5877 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5882      TCGA-BQ-5885 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-DW-7963      TCGA-DZ-6131 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-F9-A8NY      TCGA-F9-A97G      TCGA-G7-6789      TCGA-G7-6793 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LD      TCGA-GL-6846 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-GL-A9DC      TCGA-IA-A40U 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-6720      TCGA-J7-8537      TCGA-J7-A8I2 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-KV-A74V      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-P4-AAVL      TCGA-SX-A71R      TCGA-SX-A7SM      TCGA-SX-A7SP 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-UN-AAZ9      TCGA-UZ-A9PM      TCGA-UZ-A9PX 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-Y8-A897 
"IGSF3 WILD-TYPE" 
D26V6, binary
                 cls
clus               0  1
  IGSF3 MUTATED    2  0
  IGSF3 WILD-TYPE 92  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      2    0
  IGSF3 WILD-TYPE   92    9
   clus
vv  IGSF3 MUTATED IGSF3 WILD-TYPE
  0             2              92
  1             0               9
[1] 2 2
[1] FALSE
D26V7, binary
                 cls
clus                0   1
  IGSF3 MUTATED     0   4
  IGSF3 WILD-TYPE  76 202
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      0    4
  IGSF3 WILD-TYPE   76  202
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  FEMALE             0              76
  MALE               4             202
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "IGSF3 MUTATED"         
clus
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              1              75 
     TCGA-2Z-A9JL      TCGA-2Z-A9JT      TCGA-5P-A9JU      TCGA-DW-5560 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7836      TCGA-DW-7837 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-DW-7842      TCGA-SX-A71W      TCGA-UZ-A9PZ      TCGA-2Z-A9JE 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-2Z-A9JK      TCGA-2Z-A9JN      TCGA-4A-A93W      TCGA-4A-A93X 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-4A-A93Y      TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-EV-5903      TCGA-F9-A7Q0      TCGA-G7-6789      TCGA-G7-6790 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-G7-A8LB      TCGA-G7-A8LC      TCGA-G7-A8LD      TCGA-G7-A8LE 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-Q2-A5QZ      TCGA-SX-A71R      TCGA-SX-A71S      TCGA-SX-A71U 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-SX-A71V      TCGA-SX-A7SL      TCGA-SX-A7SM      TCGA-SX-A7SN 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-SX-A7SP      TCGA-SX-A7SQ      TCGA-SX-A7SR      TCGA-SX-A7SS 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
     TCGA-SX-A7SU      TCGA-UZ-A9PL      TCGA-V9-A7HT 
"IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" "IGSF3 WILD-TYPE" 
D26V9, continuous
D26V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGSF3 MUTATED                                  0     0
  IGSF3 WILD-TYPE                                2     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IGSF3 MUTATED                           2     2
  IGSF3 WILD-TYPE                        57   198
D26V11, multiclass
                                  clus
vv                                 IGSF3 MUTATED IGSF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               6
  BLACK OR AFRICAN AMERICAN                    2              57
  WHITE                                        2             198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                 cls
clus                0   1
  IGSF3 MUTATED     0   3
  IGSF3 WILD-TYPE  11 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      0    3
  IGSF3 WILD-TYPE   11  232
                        clus
vv                       IGSF3 MUTATED IGSF3 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             3             232
[1] 2 2
[1] FALSE
