[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/19775272/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/19898020/transformed.cor.cli.txt"

nPatients in clinical file=290, in cluster file=161, common to both=161
[1]  19 161
[1] "FAM18B2 MUTATION ANALYSIS"
[1] 3
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
               35               126 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
               35               126 
[1] "HNRNPM MUTATION ANALYSIS"
[1] 3
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              10              151 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              10              151 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
            10            151 
  NEFH MUTATED NEFH WILD-TYPE 
            10            151 
[1] "ZNF598 MUTATION ANALYSIS"
[1] 3
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10              151 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10              151 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           10           151 
  NF2 MUTATED NF2 WILD-TYPE 
           10           151 
[1] "TDG MUTATION ANALYSIS"
[1] 3
  TDG MUTATED TDG WILD-TYPE 
            5           156 
  TDG MUTATED TDG WILD-TYPE 
            5           156 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           15           146 
  MET MUTATED MET WILD-TYPE 
           15           146 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             11             150 
  SETD2 MUTATED SETD2 WILD-TYPE 
             11             150 
[1] "SKI MUTATION ANALYSIS"
[1] 3
  SKI MUTATED SKI WILD-TYPE 
            6           155 
  SKI MUTATED SKI WILD-TYPE 
            6           155 
[1] "MUC5B MUTATION ANALYSIS"
[1] 3
  MUC5B MUTATED MUC5B WILD-TYPE 
             14             147 
  MUC5B MUTATED MUC5B WILD-TYPE 
             14             147 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              7             154 
  KDM6A MUTATED KDM6A WILD-TYPE 
              7             154 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               8              153 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               8              153 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               157 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               157 
[1] "AHNAK2 MUTATION ANALYSIS"
[1] 3
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               7              154 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               7              154 
[1] "OR2L8 MUTATION ANALYSIS"
[1] 3
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              4             157 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              4             157 
[1] "PAM MUTATION ANALYSIS"
[1] 3
  PAM MUTATED PAM WILD-TYPE 
            3           158 
  PAM MUTATED PAM WILD-TYPE 
            3           158 
[1] "IDUA MUTATION ANALYSIS"
[1] 3
  IDUA MUTATED IDUA WILD-TYPE 
             5            156 
  IDUA MUTATED IDUA WILD-TYPE 
             5            156 
[1] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                  156 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                  156 
[1] "RPL7A MUTATION ANALYSIS"
[1] 3
  RPL7A MUTATED RPL7A WILD-TYPE 
              3             158 
  RPL7A MUTATED RPL7A WILD-TYPE 
              3             158 
[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 161 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=22,	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=136,	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=11,	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=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	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=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=19,	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 161 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=49, 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 
103  16  41   1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  103    16    42 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
103  16  41   1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  103    16    42 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
28 17  4 
[1] "table(vv)"
vv
N0 N1 N2 
28 17  4 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
28 17  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
28 17  4 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=23, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=19, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = FAM18B2 MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  FAM18B2 MUTATED    29   5
  FAM18B2 WILD-TYPE 107  17
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
               34               124 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                5                17 
$`FAM18B2 MUTATED`
TCGA-A4-7828 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-A5XZ TCGA-B3-3925 TCGA-B9-4113 
        7.82        25.64        23.31        15.75        33.83        50.50 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A5W9 TCGA-BQ-5878 TCGA-BQ-5882 
       28.18         0.46        43.99         0.16        63.72        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       40.83        26.04         0.95         7.92         2.76       123.62 
TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-7837 TCGA-DW-7839 TCGA-DZ-6131 
       50.40         7.63         7.17        37.55        13.78        79.86 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       51.19        61.02        74.60        24.89         4.01        51.78 
TCGA-G7-6797 TCGA-GL-A4EM TCGA-MH-A55W TCGA-P4-A5EB 
       25.15         1.05        34.29        99.12 

$`FAM18B2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.97        23.28        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
       16.96         8.48        16.31         8.28        12.99        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-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
       21.07        10.09        30.58        34.49        12.46        26.40 
TCGA-B9-4116 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
       20.61        22.06         2.10        19.23        17.23        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        22.92        43.20        47.80 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5892 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 
       11.97        48.26        96.92        93.34        61.28        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       26.27        11.28         7.04         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
      129.86        24.46         3.75        14.63         3.02        40.77 
TCGA-DZ-6132 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6793 
       80.88        34.19        19.00        10.68        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       39.25        71.44        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
       12.92         3.68        27.65        12.43        17.95        84.89 
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-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55Z TCGA-MH-A560 
       12.76        10.55        18.41        29.10        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
             0.16              0.10 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
           123.62            194.79 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
            25.84             20.25 
[1] "0.2 - 123.6 (25.8)" "0.1 - 194.8 (20.2)"
[1] "hr=" "1"  
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  FAM18B2 MUTATED        19        2         8        3
  FAM18B2 WILD-TYPE      77        6        28        7
D1V3, multiclass
           clus
vv          FAM18B2 MUTATED FAM18B2 WILD-TYPE
  STAGE I                19                77
  STAGE II                2                 6
  STAGE III               8                28
  STAGE IV                3                 7
[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
  FAM18B2 MUTATED   20  5    10
  FAM18B2 WILD-TYPE 83 11    32
D1V4, multiclass
       clus
vv      FAM18B2 MUTATED FAM18B2 WILD-TYPE
  T1                 20                83
  T2                  5                11
  T3+T4              10                32
[1] 3 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
  FAM18B2 MUTATED    4  3  1
  FAM18B2 WILD-TYPE 24 14  3
D1V5, multiclass
    clus
vv   FAM18B2 MUTATED FAM18B2 WILD-TYPE
  N0               4                24
  N1               3                14
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED   13  2
  FAM18B2 WILD-TYPE 50  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED     13    2
  FAM18B2 WILD-TYPE   50    4
   clus
vv  FAM18B2 MUTATED FAM18B2 WILD-TYPE
  0              13                50
  1               2                 4
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED   11 24
  FAM18B2 WILD-TYPE 36 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED     11   24
  FAM18B2 WILD-TYPE   36   90
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  FEMALE              11                36
  MALE                24                90
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
[1] "Remove cluster labels:" "FAM18B2 MUTATED"       
clus
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                2                18 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-A69E        TCGA-DW-5561 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-DW-7963        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-GL-7773        TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-P4-A5E6 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM18B2 MUTATED                                  1     0
  FAM18B2 WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM18B2 MUTATED                           8    22
  FAM18B2 WILD-TYPE                        34    80
D1V11, multiclass
                                  clus
vv                                 FAM18B2 MUTATED FAM18B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      8                34
  WHITE                                         22                80
[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
  FAM18B2 MUTATED    1 23
  FAM18B2 WILD-TYPE  5 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED      1   23
  FAM18B2 WILD-TYPE    5   98
                        clus
vv                       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              23                98
[1] 2 2
[1] FALSE

Clustering(2) Variable = HNRNPM MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  HNRNPM MUTATED    10   0
  HNRNPM WILD-TYPE 126  22
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              10              148 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
               0               22 
$`HNRNPM MUTATED`
TCGA-BQ-5887 TCGA-BQ-7055 TCGA-BQ-7062 TCGA-DW-7841 TCGA-DZ-6132 TCGA-EV-5902 
       25.35        26.27         3.81        14.63        80.88        19.00 
TCGA-G7-7502 TCGA-GL-6846 TCGA-IA-A40X TCGA-PJ-A5Z8 
       25.84       194.79        19.99        19.73 

$`HNRNPM WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       66.71        62.66        67.73         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        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-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 
       11.28         7.63         7.04         7.17        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 
      129.86        37.55        24.46        13.78         3.75         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        51.19        61.02        74.60        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-7773 
       39.25        71.44        25.15        20.52         6.38        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
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-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
        2.04        22.26        21.34        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.55        18.41        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       99.12        92.58        17.75        14.07 

  HNRNPM MUTATED HNRNPM WILD-TYPE 
            3.81             0.10 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
          194.79           129.86 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
          22.670           21.205 
[1] "3.8 - 194.8 (22.7)" "0.1 - 129.9 (21.2)"
[1] "hr="     "7.3e+07"
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  HNRNPM MUTATED         8        0         1        1
  HNRNPM WILD-TYPE      88        8        35        9
D2V3, multiclass
           clus
vv          HNRNPM MUTATED HNRNPM WILD-TYPE
  STAGE I                8               88
  STAGE II               0                8
  STAGE III              1               35
  STAGE IV               1                9
[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
  HNRNPM MUTATED    8  0     2
  HNRNPM WILD-TYPE 95 16    40
D2V4, multiclass
       clus
vv      HNRNPM MUTATED HNRNPM WILD-TYPE
  T1                 8               95
  T2                 0               16
  T3+T4              2               40
[1] 3 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
  HNRNPM MUTATED    1  1  0
  HNRNPM WILD-TYPE 27 16  4
D2V5, multiclass
[1] "Remove cluster labels:" "HNRNPM MUTATED"        
clus
  HNRNPM MUTATED HNRNPM WILD-TYPE 
               2               47 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-B1-A657       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-7966       TCGA-GL-A59R 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
D2V6, binary
                  cls
clus                0  1
  HNRNPM MUTATED    5  0
  HNRNPM WILD-TYPE 58  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      5    0
  HNRNPM WILD-TYPE   58    6
   clus
vv  HNRNPM MUTATED HNRNPM WILD-TYPE
  0              5               58
  1              0                6
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     2   8
  HNRNPM WILD-TYPE  45 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      2    8
  HNRNPM WILD-TYPE   45  106
        clus
vv       HNRNPM MUTATED HNRNPM WILD-TYPE
  FEMALE              2               45
  MALE                8              106
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPM MUTATED                                  0     0
  HNRNPM WILD-TYPE                                2     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HNRNPM MUTATED                           3     6
  HNRNPM WILD-TYPE                        39    96
D2V11, multiclass
                                  clus
vv                                 HNRNPM MUTATED HNRNPM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     3               39
  WHITE                                         6               96
[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
  HNRNPM MUTATED     0   6
  HNRNPM WILD-TYPE   6 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      0    6
  HNRNPM WILD-TYPE    6  115
                        clus
vv                       HNRNPM MUTATED HNRNPM WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              115
[1] 2 2
[1] FALSE

Clustering(3) Variable = NEFH MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  NEFH MUTATED    10   0
  NEFH WILD-TYPE 126  22
  NEFH MUTATED NEFH WILD-TYPE 
            10            148 
  NEFH MUTATED NEFH WILD-TYPE 
             0             22 
$`NEFH MUTATED`
TCGA-A4-A5DU TCGA-B9-4117 TCGA-B9-A5W8 TCGA-GL-A59T TCGA-HE-A5NK TCGA-HE-A5NL 
       16.31         0.46        17.23        17.95        73.25        25.22 
TCGA-IA-A40X TCGA-MH-A55Z TCGA-MH-A560 TCGA-P4-A5EB 
       19.99        27.78        30.38        99.12 

$`NEFH WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A5XZ 
       19.73        14.33        12.46        16.96         8.48        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 
       20.61        43.99        22.06         2.10        19.23         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       74.60        34.19        19.00        24.89        10.68         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-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       20.52        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
       27.65         1.05        12.43        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       56.75        16.80         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  NEFH MUTATED NEFH WILD-TYPE 
          0.46           0.10 
  NEFH MUTATED NEFH WILD-TYPE 
         99.12         194.79 
  NEFH MUTATED NEFH WILD-TYPE 
        22.605         21.205 
[1] "0.5 - 99.1 (22.6)"  "0.1 - 194.8 (21.2)"
[1] "hr="     "7.3e+07"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         7        1         0        0
  NEFH WILD-TYPE      89        7        36       10
D3V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              7             89
  STAGE II             1              7
  STAGE III            0             36
  STAGE IV             0             10
[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    8  2     0
  NEFH WILD-TYPE 95 14    42
D3V4, multiclass
       clus
vv      NEFH MUTATED NEFH WILD-TYPE
  T1               8             95
  T2               2             14
  T3+T4            0             42
[1] 3 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    0  0  0
  NEFH WILD-TYPE 28 17  4
D3V5, multiclass
D3V6, binary
                cls
clus              0  1
  NEFH MUTATED    2  0
  NEFH WILD-TYPE 61  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      2    0
  NEFH WILD-TYPE   61    6
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            2             61
  1            0              6
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus               0   1
  NEFH MUTATED     3   7
  NEFH WILD-TYPE  44 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      3    7
  NEFH WILD-TYPE   44  107
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            3             44
  MALE              7            107
[1] 2 2
[1] FALSE
D3V8, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2             42 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098     TCGA-A4-8310 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8517     TCGA-A4-8518 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-8630     TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466     TCGA-DW-5560 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-7502     TCGA-G7-A4TM     TCGA-IA-A40U     TCGA-IA-A40Y 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-J7-8537     TCGA-Q2-A5QZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" 
D3V9, continuous
D3V10, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             1             19 
    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-A69E 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-6793     TCGA-G7-6795 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-7501     TCGA-GL-7773     TCGA-HE-A5NI     TCGA-IA-A40U 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEFH MUTATED                                  0     0
  NEFH WILD-TYPE                                2     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED                           4     4
  NEFH WILD-TYPE                        38    98
D3V11, multiclass
                                  clus
vv                                 NEFH MUTATED NEFH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   4             38
  WHITE                                       4             98
[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
  NEFH MUTATED     0   8
  NEFH WILD-TYPE   6 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    8
  NEFH WILD-TYPE    6  113
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            113
[1] 2 2
[1] FALSE

Clustering(4) Variable = ZNF598 MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2                0   1
  ZNF598 MUTATED     7   3
  ZNF598 WILD-TYPE 129  19
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10              148 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               3               19 
$`ZNF598 MUTATED`
TCGA-AL-3473 TCGA-AT-A5NU TCGA-B3-8121 TCGA-BQ-5877 TCGA-BQ-5893 TCGA-DW-7834 
       62.66         2.20        12.46         8.88         7.92       129.86 
TCGA-DW-7838 TCGA-EV-5903 TCGA-G7-7501 TCGA-G7-7502 
       24.46        24.89        20.52        25.84 

$`ZNF598 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       66.71        67.73        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       34.49        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        17.23         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       14.86        86.76        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-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.66         0.95        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 
        7.17         3.81        48.85        13.61        37.55        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ 
       51.19        61.02        74.60        34.19        19.00        10.68 
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-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.15         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        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-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  ZNF598 MUTATED ZNF598 WILD-TYPE 
             2.2              0.1 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
          129.86           194.79 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
          22.490           21.205 
[1] "2.2 - 129.9 (22.5)" "0.1 - 194.8 (21.2)"
[1] "hr=" "2.5"
D4V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF598 MUTATED         6        1         1        2
  ZNF598 WILD-TYPE      90        7        35        8
D4V3, multiclass
           clus
vv          ZNF598 MUTATED ZNF598 WILD-TYPE
  STAGE I                6               90
  STAGE II               1                7
  STAGE III              1               35
  STAGE IV               2                8
[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
  ZNF598 MUTATED    6  1     3
  ZNF598 WILD-TYPE 97 15    39
D4V4, multiclass
       clus
vv      ZNF598 MUTATED ZNF598 WILD-TYPE
  T1                 6               97
  T2                 1               15
  T3+T4              3               39
[1] 3 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
  ZNF598 MUTATED    1  3  0
  ZNF598 WILD-TYPE 27 14  4
D4V5, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  N0              1               27
  N1              3               14
  N2              0                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                  cls
clus                0  1
  ZNF598 MUTATED    2  2
  ZNF598 WILD-TYPE 61  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      2    2
  ZNF598 WILD-TYPE   61    4
   clus
vv  ZNF598 MUTATED ZNF598 WILD-TYPE
  0              2               61
  1              2                4
[1] 2 2
[1] FALSE
D4V7, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     2   8
  ZNF598 WILD-TYPE  45 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      2    8
  ZNF598 WILD-TYPE   45  106
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  FEMALE              2               45
  MALE                8              106
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
[1] "Remove cluster labels:" "ZNF598 MUTATED"        
clus
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               1               19 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-B9-A69E       TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-6793 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-G7-6795       TCGA-GL-7773       TCGA-HE-A5NI       TCGA-IA-A40U 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF598 MUTATED                                  0     0
  ZNF598 WILD-TYPE                                2     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF598 MUTATED                           3     7
  ZNF598 WILD-TYPE                        39    95
D4V11, multiclass
                                  clus
vv                                 ZNF598 MUTATED ZNF598 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     3               39
  WHITE                                         7               95
[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
  ZNF598 MUTATED     1   8
  ZNF598 WILD-TYPE   5 113
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      1    8
  ZNF598 WILD-TYPE    5  113
                        clus
vv                       ZNF598 MUTATED ZNF598 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              8              113
[1] 2 2
[1] FALSE

Clustering(5) Variable = NF2 MUTATION ANALYSIS
D5V1, survival
               sevent
clus2             0   1
  NF2 MUTATED     8   2
  NF2 WILD-TYPE 128  20
  NF2 MUTATED NF2 WILD-TYPE 
           10           148 
  NF2 MUTATED NF2 WILD-TYPE 
            2            20 
$`NF2 MUTATED`
TCGA-A4-8098 TCGA-B1-A47M TCGA-B9-4117 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5894 
       29.46        21.67         0.46        86.76         8.88         2.76 
TCGA-EV-5902 TCGA-G7-6797 TCGA-GL-7966 TCGA-P4-A5EA 
       19.00        25.15         3.68         6.61 

$`NF2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         0.23        16.64        30.48 
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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
       62.66        67.73         2.20        19.56        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        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-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        17.23         0.16 
TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       14.86        19.27        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.66         0.95        11.97         7.92 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       80.88        51.19        61.02        74.60        34.19        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       71.44        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        84.89        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-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
        2.04        22.26        21.34        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.55        18.41        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       27.65        20.25        99.78        87.09        42.94        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  NF2 MUTATED NF2 WILD-TYPE 
         0.46          0.10 
  NF2 MUTATED NF2 WILD-TYPE 
        86.76        194.79 
  NF2 MUTATED NF2 WILD-TYPE 
       13.940        21.355 
[1] "0.5 - 86.8 (13.9)"  "0.1 - 194.8 (21.4)"
[1] "hr=" "2.4"
D5V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         2        0         5        2
  NF2 WILD-TYPE      94        8        31        8
D5V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             2            94
  STAGE II            0             8
  STAGE III           5            31
  STAGE IV            2             8
[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 100  15    36
D5V4, multiclass
       clus
vv      NF2 MUTATED NF2 WILD-TYPE
  T1              3           100
  T2              1            15
  T3+T4           6            36
[1] 3 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  4  0
  NF2 WILD-TYPE 28 13  4
D5V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0           0            28
  N1           4            13
  N2           0             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
               cls
clus             0  1
  NF2 MUTATED    2  2
  NF2 WILD-TYPE 61  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      2    2
  NF2 WILD-TYPE   61    4
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           2            61
  1           2             4
[1] 2 2
[1] FALSE
D5V7, binary
               cls
clus              0   1
  NF2 MUTATED     4   6
  NF2 WILD-TYPE  43 108
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      4    6
  NF2 WILD-TYPE   43  108
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           4            43
  MALE             6           108
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            1            32 
   TCGA-A4-8310    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4115 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-7268    TCGA-B9-A44B    TCGA-B9-A69E    TCGA-DW-5561    TCGA-DW-7834 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7838    TCGA-DW-7963    TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-7501    TCGA-GL-7773    TCGA-GL-A59T    TCGA-HE-A5NI    TCGA-HE-A5NJ 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-HE-A5NK    TCGA-IA-A40U    TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" 
D5V10, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            1            19 
   TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3472    TCGA-AL-7173 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-A69E    TCGA-DW-5561    TCGA-DW-7963 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-7773    TCGA-HE-A5NI 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IA-A40U    TCGA-P4-A5E6    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF2 MUTATED                                  0     0
  NF2 WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED                           4     5
  NF2 WILD-TYPE                        38    97
D5V11, multiclass
                                  clus
vv                                 NF2 MUTATED NF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  4            38
  WHITE                                      5            97
[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
  NF2 MUTATED     1   6
  NF2 WILD-TYPE   5 115
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      1    6
  NF2 WILD-TYPE    5  115
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO           6           115
[1] 2 2
[1] FALSE

Clustering(6) Variable = TDG MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  TDG MUTATED     5   0
  TDG WILD-TYPE 131  22
  TDG MUTATED TDG WILD-TYPE 
            5           153 
  TDG MUTATED TDG WILD-TYPE 
            0            22 
$`TDG MUTATED`
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-7840 TCGA-GL-6846 
        0.95        11.97        96.92         3.75       194.79 

$`TDG WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       66.71        62.66        67.73         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.82         7.66         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
      129.86        37.55        24.46        13.78        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         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-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       25.84         6.38        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
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-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  TDG MUTATED TDG WILD-TYPE 
         0.95          0.10 
  TDG MUTATED TDG WILD-TYPE 
       194.79        129.86 
  TDG MUTATED TDG WILD-TYPE 
        11.97         21.34 
[1] "0.9 - 194.8 (12.0)" "0.1 - 129.9 (21.3)"
[1] "hr="     "2.6e+07"
D6V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  TDG MUTATED         3        0         1        1
  TDG WILD-TYPE      93        8        35        9
D6V3, multiclass
           clus
vv          TDG MUTATED TDG WILD-TYPE
  STAGE I             3            93
  STAGE II            0             8
  STAGE III           1            35
  STAGE IV            1             9
[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
  TDG MUTATED     3   0     2
  TDG WILD-TYPE 100  16    40
D6V4, multiclass
       clus
vv      TDG MUTATED TDG WILD-TYPE
  T1              3           100
  T2              0            16
  T3+T4           2            40
[1] 3 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
  TDG MUTATED    2  1  0
  TDG WILD-TYPE 26 16  4
D6V5, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  N0           2            26
  N1           1            16
  N2           0             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
               cls
clus             0  1
  TDG MUTATED    3  0
  TDG WILD-TYPE 60  6
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      3    0
  TDG WILD-TYPE   60    6
   clus
vv  TDG MUTATED TDG WILD-TYPE
  0           3            60
  1           0             6
[1] 2 2
[1] FALSE
D6V7, binary
               cls
clus              0   1
  TDG MUTATED     1   4
  TDG WILD-TYPE  46 110
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      1    4
  TDG WILD-TYPE   46  110
        clus
vv       TDG MUTATED TDG WILD-TYPE
  FEMALE           1            46
  MALE             4           110
[1] 2 2
[1] FALSE
D6V8, continuous
[1] "Remove cluster labels:" "TDG MUTATED"           
clus
  TDG MUTATED TDG WILD-TYPE 
            1            43 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8311 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-A4-8312    TCGA-A4-8517    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A48D 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU    TCGA-A4-A5XZ    TCGA-A4-A6HP 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-EV-5901    TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40U    TCGA-IA-A40X 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-IA-A40Y    TCGA-J7-8537    TCGA-Q2-A5QZ 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
D6V9, continuous
D6V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TDG MUTATED                                  0     0
  TDG WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TDG MUTATED                           1     4
  TDG WILD-TYPE                        41    98
D6V11, multiclass
                                  clus
vv                                 TDG MUTATED TDG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  1            41
  WHITE                                      4            98
[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
  TDG MUTATED     0   4
  TDG WILD-TYPE   6 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      0    4
  TDG WILD-TYPE    6  117
                        clus
vv                       TDG MUTATED TDG WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           4           117
[1] 2 2
[1] FALSE

Clustering(7) Variable = MET MUTATION ANALYSIS
D7V1, survival
               sevent
clus2             0   1
  MET MUTATED    14   1
  MET WILD-TYPE 122  21
  MET MUTATED MET WILD-TYPE 
           15           143 
  MET MUTATED MET WILD-TYPE 
            1            21 
$`MET MUTATED`
TCGA-A4-7734 TCGA-A4-7997 TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-A654 TCGA-B9-4117 
        0.89        30.48        66.71        67.73        20.25         0.46 
TCGA-BQ-5882 TCGA-BQ-7059 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-GL-A59R TCGA-HE-A5NH 
       21.63         7.63        80.88        74.60        12.43        26.01 
TCGA-IA-A40U TCGA-IZ-8196 TCGA-MH-A561 
       16.80        21.34        27.65 

$`MET WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 
       19.13         7.82         0.23        16.64        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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-AT-A5NU 
       12.99        12.46         9.63        70.19        62.66         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       19.56        21.67        24.56        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       28.18        26.40        20.61        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       26.27        11.28         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        79.86        51.19        61.02 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         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-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        1.05        17.95        84.89        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       25.22        19.99         2.04        22.26        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       30.38        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       99.12        92.58        19.73        17.75        14.07 

  MET MUTATED MET WILD-TYPE 
         0.46          0.10 
  MET MUTATED MET WILD-TYPE 
        80.88        194.79 
  MET MUTATED MET WILD-TYPE 
        21.63         20.61 
[1] "0.5 - 80.9 (21.6)"  "0.1 - 194.8 (20.6)"
[1] "hr=" "2.4"
D7V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  MET MUTATED         9        0         3        1
  MET WILD-TYPE      87        8        33        9
D7V3, multiclass
           clus
vv          MET MUTATED MET WILD-TYPE
  STAGE I             9            87
  STAGE II            0             8
  STAGE III           3            33
  STAGE IV            1             9
[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    9  2     4
  MET WILD-TYPE 94 14    38
D7V4, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  T1              9            94
  T2              2            14
  T3+T4           4            38
[1] 3 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    4  0  1
  MET WILD-TYPE 24 17  3
D7V5, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  N0           4            24
  N1           0            17
  N2           1             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
               cls
clus             0  1
  MET MUTATED    6  0
  MET WILD-TYPE 57  6
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      6    0
  MET WILD-TYPE   57    6
   clus
vv  MET MUTATED MET WILD-TYPE
  0           6            57
  1           0             6
[1] 2 2
[1] FALSE
D7V7, binary
               cls
clus              0   1
  MET MUTATED     4  11
  MET WILD-TYPE  43 103
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      4   11
  MET WILD-TYPE   43  103
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           4            43
  MALE            11           103
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "MET MUTATED"           
clus
  MET MUTATED MET WILD-TYPE 
            1            43 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8311 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-8312    TCGA-A4-8517    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A48D 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU    TCGA-A4-A5XZ    TCGA-A4-A6HP 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-G7-6797    TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40X 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-IA-A40Y    TCGA-J7-8537    TCGA-Q2-A5QZ 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
D7V9, continuous
D7V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           3     8
  MET WILD-TYPE                        39    94
D7V11, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  3            39
  WHITE                                      8            94
[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
  MET MUTATED     1  10
  MET WILD-TYPE   5 111
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      1   10
  MET WILD-TYPE    5  111
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          10           111
[1] 2 2
[1] FALSE

Clustering(8) Variable = SETD2 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED     8   3
  SETD2 WILD-TYPE 128  19
  SETD2 MUTATED SETD2 WILD-TYPE 
             11             147 
  SETD2 MUTATED SETD2 WILD-TYPE 
              3              19 
$`SETD2 MUTATED`
TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-B1-A656 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5876 
       29.46        12.99        20.32         2.10        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7058 TCGA-BQ-7061 
        8.88         7.66         0.95        11.28         7.17 

$`SETD2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         0.23        16.64        30.48 
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-A47M TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        21.07        33.83        10.09        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06        19.23        17.23         0.16        14.86 
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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
       93.34        61.28        50.40        49.84        26.27         7.63 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.04         3.81        48.85        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         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-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
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-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.95            0.10 
  SETD2 MUTATED SETD2 WILD-TYPE 
          86.76          194.79 
  SETD2 MUTATED SETD2 WILD-TYPE 
          11.28           21.67 
[1] "0.9 - 86.8 (11.3)"  "0.1 - 194.8 (21.7)"
[1] "hr=" "3.7"
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED         4        0         6        1
  SETD2 WILD-TYPE      92        8        30        9
D8V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I               4              92
  STAGE II              0               8
  STAGE III             6              30
  STAGE IV              1               9
[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    5  0     6
  SETD2 WILD-TYPE 98 16    36
D8V4, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  T1                5              98
  T2                0              16
  T3+T4             6              36
[1] 3 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    3  2  1
  SETD2 WILD-TYPE 25 15  3
D8V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0             3              25
  N1             2              15
  N2             1               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                 cls
clus               0  1
  SETD2 MUTATED    7  1
  SETD2 WILD-TYPE 56  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      7    1
  SETD2 WILD-TYPE   56    5
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0             7              56
  1             1               5
[1] 2 2
[1] FALSE
D8V7, binary
                 cls
clus                0   1
  SETD2 MUTATED     3   8
  SETD2 WILD-TYPE  44 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      3    8
  SETD2 WILD-TYPE   44  106
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE             3              44
  MALE               8             106
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              43 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-5560 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
D8V9, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              32 
     TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173      TCGA-B1-A654 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4117      TCGA-B9-7268 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DW-7963      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T      TCGA-HE-A5NI 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U      TCGA-IZ-A6M8 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
D8V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     0
  SETD2 WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           3     8
  SETD2 WILD-TYPE                        39    94
D8V11, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    3              39
  WHITE                                        8              94
[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
  SETD2 MUTATED     0   8
  SETD2 WILD-TYPE   6 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      0    8
  SETD2 WILD-TYPE    6  113
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             113
[1] 2 2
[1] FALSE

Clustering(9) Variable = SKI MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  SKI MUTATED     5   1
  SKI WILD-TYPE 131  21
  SKI MUTATED SKI WILD-TYPE 
            6           152 
  SKI MUTATED SKI WILD-TYPE 
            1            21 
$`SKI MUTATED`
TCGA-A4-7585 TCGA-B9-7268 TCGA-BQ-5884 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
       35.18        22.06        26.04        80.88        61.02        74.60 

$`SKI WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        21.37        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
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-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       20.61         0.46        43.99         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        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-5885 
       22.92        43.20        47.80        21.63        40.83        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5902 
        3.02        40.77        79.86        51.19        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         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         6.38 
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-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       25.22        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.09        42.94         6.61        99.12        92.58        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  SKI MUTATED SKI WILD-TYPE 
        22.06          0.10 
  SKI MUTATED SKI WILD-TYPE 
        80.88        194.79 
  SKI MUTATED SKI WILD-TYPE 
        48.10         20.42 
[1] "22.1 - 80.9 (48.1)" "0.1 - 194.8 (20.4)"
[1] "hr=" "1.4"
D9V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  SKI MUTATED         4        1         1        0
  SKI WILD-TYPE      92        7        35       10
D9V3, multiclass
           clus
vv          SKI MUTATED SKI WILD-TYPE
  STAGE I             4            92
  STAGE II            1             7
  STAGE III           1            35
  STAGE IV            0            10
[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
  SKI MUTATED    4  1     1
  SKI WILD-TYPE 99 15    41
D9V4, multiclass
       clus
vv      SKI MUTATED SKI WILD-TYPE
  T1              4            99
  T2              1            15
  T3+T4           1            41
[1] 3 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
  SKI MUTATED    2  0  0
  SKI WILD-TYPE 26 17  4
D9V5, multiclass
[1] "Remove cluster labels:" "SKI MUTATED"           
clus
  SKI MUTATED SKI WILD-TYPE 
            2            47 
   TCGA-A4-7583    TCGA-A4-7915    TCGA-A4-A57E    TCGA-A4-A5Y1    TCGA-AL-3466 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173    TCGA-B1-5398    TCGA-B1-A655 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-B1-A656    TCGA-B1-A657    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5882    TCGA-BQ-5885    TCGA-BQ-5887    TCGA-BQ-5888 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-5889    TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-5894    TCGA-BQ-7045    TCGA-BQ-7048    TCGA-BQ-7050    TCGA-BQ-7051 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-7058    TCGA-DW-7963    TCGA-DZ-6131    TCGA-G7-6789    TCGA-G7-6793 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-6846    TCGA-GL-7966    TCGA-GL-A59R 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-IA-A40U    TCGA-IA-A40Y    TCGA-J7-6720    TCGA-J7-8537    TCGA-P4-A5E6 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-P4-A5E8    TCGA-P4-A5EA 
"SKI WILD-TYPE" "SKI WILD-TYPE" 
D9V6, binary
               cls
clus             0  1
  SKI MUTATED    3  0
  SKI WILD-TYPE 60  6
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      3    0
  SKI WILD-TYPE   60    6
   clus
vv  SKI MUTATED SKI WILD-TYPE
  0           3            60
  1           0             6
[1] 2 2
[1] FALSE
D9V7, binary
               cls
clus              0   1
  SKI MUTATED     1   5
  SKI WILD-TYPE  46 109
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      1    5
  SKI WILD-TYPE   46  109
        clus
vv       SKI MUTATED SKI WILD-TYPE
  FEMALE           1            46
  MALE             5           109
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
[1] "Remove cluster labels:" "SKI MUTATED"           
clus
  SKI MUTATED SKI WILD-TYPE 
            1            32 
   TCGA-A4-8310    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4115 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-A44B    TCGA-B9-A69E    TCGA-DW-5561    TCGA-DW-7834 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-DW-7838    TCGA-DW-7963    TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-G7-7501    TCGA-GL-7773    TCGA-GL-A59T    TCGA-HE-A5NI    TCGA-HE-A5NJ 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-HE-A5NK    TCGA-IA-A40U    TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"SKI WILD-TYPE" "SKI WILD-TYPE" 
D9V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKI MUTATED                                  0     0
  SKI WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SKI MUTATED                           1     3
  SKI WILD-TYPE                        41    99
D9V11, multiclass
                                  clus
vv                                 SKI MUTATED SKI WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  1            41
  WHITE                                      3            99
[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
  SKI MUTATED     0   2
  SKI WILD-TYPE   6 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      0    2
  SKI WILD-TYPE    6  119
                        clus
vv                       SKI MUTATED SKI WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           2           119
[1] 2 2
[1] FALSE

Clustering(10) Variable = MUC5B MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  MUC5B MUTATED    11   3
  MUC5B WILD-TYPE 125  19
  MUC5B MUTATED MUC5B WILD-TYPE 
             14             144 
  MUC5B MUTATED MUC5B WILD-TYPE 
              3              19 
$`MUC5B MUTATED`
TCGA-A4-7288 TCGA-A4-7828 TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 
       61.05         7.82        23.97        19.73         8.48         8.28 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-A47N TCGA-BQ-5888 TCGA-BQ-7044 TCGA-BQ-7062 
       12.99         9.63        24.56        13.25       123.62         3.81 
TCGA-DW-7963 TCGA-P4-A5E7 
       40.77        87.09 

$`MUC5B WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.28        23.31        19.63        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       16.31        15.75        12.46        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A654 TCGA-B1-A655 
       67.73         2.20        19.56        21.67        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        33.83        10.09        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-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        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-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        25.35        10.82         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        7.17        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.78         3.75        14.63         3.02        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         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-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E8 
       27.78        30.38        27.65        20.25        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  MUC5B MUTATED MUC5B WILD-TYPE 
           3.81            0.10 
  MUC5B MUTATED MUC5B WILD-TYPE 
         123.62          194.79 
  MUC5B MUTATED MUC5B WILD-TYPE 
         16.490          21.355 
[1] "3.8 - 123.6 (16.5)" "0.1 - 194.8 (21.4)"
[1] "hr=" "1.8"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MUC5B MUTATED         9        0         2        2
  MUC5B WILD-TYPE      87        8        34        8
D10V3, multiclass
           clus
vv          MUC5B MUTATED MUC5B WILD-TYPE
  STAGE I               9              87
  STAGE II              0               8
  STAGE III             2              34
  STAGE IV              2               8
[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
  MUC5B MUTATED   11  1     2
  MUC5B WILD-TYPE 92 15    40
D10V4, multiclass
       clus
vv      MUC5B MUTATED MUC5B WILD-TYPE
  T1               11              92
  T2                1              15
  T3+T4             2              40
[1] 3 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
  MUC5B MUTATED    3  2  0
  MUC5B WILD-TYPE 25 15  4
D10V5, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  N0             3              25
  N1             2              15
  N2             0               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                 cls
clus               0  1
  MUC5B MUTATED    4  2
  MUC5B WILD-TYPE 59  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      4    2
  MUC5B WILD-TYPE   59    4
   clus
vv  MUC5B MUTATED MUC5B WILD-TYPE
  0             4              59
  1             2               4
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus                0   1
  MUC5B MUTATED     5   9
  MUC5B WILD-TYPE  42 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      5    9
  MUC5B WILD-TYPE   42  105
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  FEMALE             5              42
  MALE               9             105
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC5B MUTATED                                  0     0
  MUC5B WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUC5B MUTATED                           3    11
  MUC5B WILD-TYPE                        39    91
D10V11, multiclass
                                  clus
vv                                 MUC5B MUTATED MUC5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    3              39
  WHITE                                       11              91
[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"
D10V12, binary
                 cls
clus                0   1
  MUC5B MUTATED     0  12
  MUC5B WILD-TYPE   6 109
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      0   12
  MUC5B WILD-TYPE    6  109
                        clus
vv                       MUC5B MUTATED MUC5B WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             109
[1] 2 2
[1] FALSE

Clustering(11) Variable = KDM6A MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     5   0
  KDM6A WILD-TYPE 131  22
  KDM6A MUTATED KDM6A WILD-TYPE 
              5             153 
  KDM6A MUTATED KDM6A WILD-TYPE 
              0              22 
$`KDM6A MUTATED`
TCGA-A4-7584 TCGA-A4-A48D TCGA-BQ-5886 TCGA-BQ-7060 TCGA-IZ-A6M8 
       21.37        12.46        26.04         7.04        16.34 

$`KDM6A WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         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-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       14.33        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        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-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        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-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.17         3.81        48.85        13.61       129.86 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         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-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        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-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-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
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-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  KDM6A MUTATED KDM6A WILD-TYPE 
           7.04            0.10 
  KDM6A MUTATED KDM6A WILD-TYPE 
          26.04          194.79 
  KDM6A MUTATED KDM6A WILD-TYPE 
          16.34           21.34 
[1] "7.0 - 26.0 (16.3)"  "0.1 - 194.8 (21.3)"
[1] "hr="     "9300000"
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         5        0         2        0
  KDM6A WILD-TYPE      91        8        34       10
D11V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               5              91
  STAGE II              0               8
  STAGE III             2              34
  STAGE IV              0              10
[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    4  1     2
  KDM6A WILD-TYPE 99 15    40
D11V4, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  T1                4              99
  T2                1              15
  T3+T4             2              40
[1] 3 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    0  0  0
  KDM6A WILD-TYPE 28 17  4
D11V5, multiclass
D11V6, binary
                 cls
clus               0  1
  KDM6A MUTATED    4  0
  KDM6A WILD-TYPE 59  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      4    0
  KDM6A WILD-TYPE   59    6
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             4              59
  1             0               6
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus                0   1
  KDM6A MUTATED     1   6
  KDM6A WILD-TYPE  46 108
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1    6
  KDM6A WILD-TYPE   46  108
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             1              46
  MALE               6             108
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              43 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-5560 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
D11V9, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              2              31 
     TCGA-A4-8310      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3466 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B9-4115      TCGA-B9-4117      TCGA-B9-7268      TCGA-B9-A44B 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7963      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T      TCGA-HE-A5NI 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U      TCGA-P4-A5E7 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-P4-A5EB      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
D11V10, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              19 
     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-5561      TCGA-DW-7963      TCGA-G7-6793      TCGA-G7-6795 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-7773      TCGA-HE-A5NI      TCGA-IA-A40U 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  1     0
  KDM6A WILD-TYPE                                1     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           3     1
  KDM6A WILD-TYPE                        39   101
D11V11, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    3              39
  WHITE                                        1             101
[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
  KDM6A MUTATED     0   4
  KDM6A WILD-TYPE   6 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    4
  KDM6A WILD-TYPE    6  117
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             117
[1] 2 2
[1] FALSE

Clustering(12) Variable = ZNF814 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  ZNF814 MUTATED     7   1
  ZNF814 WILD-TYPE 129  21
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               8              150 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1               21 
$`ZNF814 MUTATED`
TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-DW-7840 TCGA-G7-A4TM TCGA-GL-A4EM TCGA-IZ-8195 
       12.99         2.10         3.75         6.38         1.05        22.26 
TCGA-KV-A6GE TCGA-P4-A5EB 
       29.10        99.12 

$`ZNF814 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
       20.61         0.46        43.99        22.06        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 
       13.61       129.86        37.55        24.46        13.78        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       74.60        34.19        19.00        24.89        10.68         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-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       20.52        25.84       194.79        12.92         3.68        27.65 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8196 
       73.25        25.22        16.80        19.99         2.04        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A55W 
       16.34        12.36        12.76        10.55        18.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       42.94         6.61        92.58        19.73        17.75        14.07 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
            1.05             0.10 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           99.12           194.79 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           9.685           21.355 
[1] "1.1 - 99.1 (9.7)"   "0.1 - 194.8 (21.4)"
[1] "hr=" "1.5"
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         5        1         2        0
  ZNF814 WILD-TYPE      91        7        34       10
D12V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                5               91
  STAGE II               1                7
  STAGE III              2               34
  STAGE IV               0               10
[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     1
  ZNF814 WILD-TYPE 97 15    41
D12V4, multiclass
       clus
vv      ZNF814 MUTATED ZNF814 WILD-TYPE
  T1                 6               97
  T2                 1               15
  T3+T4              1               41
[1] 3 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  0
  ZNF814 WILD-TYPE 28 16  4
D12V5, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1               48 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       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-GL-6846       TCGA-GL-7966 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
D12V6, binary
                  cls
clus                0  1
  ZNF814 MUTATED    0  0
  ZNF814 WILD-TYPE 63  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    0
  ZNF814 WILD-TYPE   63    6
D12V7, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     0   8
  ZNF814 WILD-TYPE  47 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    8
  ZNF814 WILD-TYPE   47  106
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              0               47
  MALE                8              106
[1] 2 2
[1] FALSE
D12V8, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               42 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834       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-DW-7963       TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-7502       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-J7-8537       TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
D12V9, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               31 
      TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173       TCGA-B1-A654 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117       TCGA-B9-7268 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B9-A69E       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7963       TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-7773       TCGA-GL-A59T       TCGA-HE-A5NI 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U       TCGA-IZ-A6M8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-P4-A5E7       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
D12V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF814 MUTATED                                  0     0
  ZNF814 WILD-TYPE                                2     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF814 MUTATED                           3     5
  ZNF814 WILD-TYPE                        39    97
D12V11, multiclass
                                  clus
vv                                 ZNF814 MUTATED ZNF814 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     3               39
  WHITE                                         5               97
[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
  ZNF814 MUTATED     0   8
  ZNF814 WILD-TYPE   6 113
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    8
  ZNF814 WILD-TYPE    6  113
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              113
[1] 2 2
[1] FALSE

Clustering(13) Variable = SMARCB1 MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED     4   0
  SMARCB1 WILD-TYPE 132  22
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               154 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                0                22 
$`SMARCB1 MUTATED`
TCGA-B1-A47M TCGA-BQ-5876 TCGA-BQ-7048 TCGA-GL-6846 
       21.67        19.27        93.34       194.79 

$`SMARCB1 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        19.56        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
       17.23         0.16        14.86        86.76         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       96.92        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       74.60        34.19        19.00        24.89        10.68         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-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       20.52        25.84         6.38        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        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-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            19.27              0.10 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           194.79            129.86 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           57.505            20.840 
[1] "19.3 - 194.8 (57.5)" "0.1 - 129.9 (20.8)" 
[1] "hr="     "2.6e+07"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SMARCB1 MUTATED         1        0         2        1
  SMARCB1 WILD-TYPE      95        8        34        9
D13V3, multiclass
           clus
vv          SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                 1                95
  STAGE II                0                 8
  STAGE III               2                34
  STAGE IV                1                 9
[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     1   0     3
  SMARCB1 WILD-TYPE 102  16    39
D13V4, multiclass
       clus
vv      SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1                  1               102
  T2                  0                16
  T3+T4               3                39
[1] 3 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    1  1  0
  SMARCB1 WILD-TYPE 27 16  4
D13V5, multiclass
[1] "Remove cluster labels:" "SMARCB1 MUTATED"       
clus
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                2                47 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-A5Y1        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-B1-A657        TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7058 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789        TCGA-G7-6793 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-7966        TCGA-GL-A59R 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720        TCGA-J7-8537 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-A5E8        TCGA-P4-A5EA 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
D13V6, binary
                   cls
clus                 0  1
  SMARCB1 MUTATED    2  0
  SMARCB1 WILD-TYPE 61  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      2    0
  SMARCB1 WILD-TYPE   61    6
   clus
vv  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  0               2                61
  1               0                 6
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     0   4
  SMARCB1 WILD-TYPE  47 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0    4
  SMARCB1 WILD-TYPE   47  110
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE               0                47
  MALE                 4               110
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCB1 MUTATED                                  0     0
  SMARCB1 WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCB1 MUTATED                           1     3
  SMARCB1 WILD-TYPE                        41    99
D13V11, multiclass
                                  clus
vv                                 SMARCB1 MUTATED SMARCB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      1                41
  WHITE                                          3                99
[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
  SMARCB1 MUTATED     0   3
  SMARCB1 WILD-TYPE   6 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0    3
  SMARCB1 WILD-TYPE    6  118
                        clus
vv                       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               3               118
[1] 2 2
[1] FALSE

Clustering(14) Variable = AHNAK2 MUTATION ANALYSIS
D14V1, survival
                  sevent
clus2                0   1
  AHNAK2 MUTATED     6   1
  AHNAK2 WILD-TYPE 130  21
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               7              151 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               1               21 
$`AHNAK2 MUTATED`
TCGA-B1-5398 TCGA-B9-4117 TCGA-BQ-5882 TCGA-BQ-7060 TCGA-DZ-6135 TCGA-EV-5901 
       19.56         0.46        21.63         7.04        74.60        34.19 
TCGA-GL-7773 
       12.92 

$`AHNAK2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       20.61        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.17         3.81        48.85        13.61       129.86 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5902 
       40.77        79.86        80.88        51.19        61.02        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         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         6.38 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
            0.46             0.10 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
           74.60           194.79 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
           19.56            21.34 
[1] "0.5 - 74.6 (19.6)"  "0.1 - 194.8 (21.3)"
[1] "hr=" "1.3"
D14V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  AHNAK2 MUTATED         4        0         2        0
  AHNAK2 WILD-TYPE      92        8        34       10
D14V3, multiclass
           clus
vv          AHNAK2 MUTATED AHNAK2 WILD-TYPE
  STAGE I                4               92
  STAGE II               0                8
  STAGE III              2               34
  STAGE IV               0               10
[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
  AHNAK2 MUTATED    4  1     2
  AHNAK2 WILD-TYPE 99 15    40
D14V4, multiclass
       clus
vv      AHNAK2 MUTATED AHNAK2 WILD-TYPE
  T1                 4               99
  T2                 1               15
  T3+T4              2               40
[1] 3 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
  AHNAK2 MUTATED    2  0  0
  AHNAK2 WILD-TYPE 26 17  4
D14V5, multiclass
[1] "Remove cluster labels:" "AHNAK2 MUTATED"        
clus
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               2               47 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5885       TCGA-BQ-5887       TCGA-BQ-5888 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891       TCGA-BQ-5892 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058       TCGA-DW-7963 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793       TCGA-G7-6795 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966       TCGA-GL-A59R 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
D14V6, binary
                  cls
clus                0  1
  AHNAK2 MUTATED    4  0
  AHNAK2 WILD-TYPE 59  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED      4    0
  AHNAK2 WILD-TYPE   59    6
   clus
vv  AHNAK2 MUTATED AHNAK2 WILD-TYPE
  0              4               59
  1              0                6
[1] 2 2
[1] FALSE
D14V7, binary
                  cls
clus                 0   1
  AHNAK2 MUTATED     2   5
  AHNAK2 WILD-TYPE  45 109
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED      2    5
  AHNAK2 WILD-TYPE   45  109
        clus
vv       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  FEMALE              2               45
  MALE                5              109
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "AHNAK2 MUTATED"        
clus
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               1               43 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7837 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5902       TCGA-EV-5903 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-IA-A40U       TCGA-IA-A40X 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
D14V9, continuous
[1] "Remove cluster labels:" "AHNAK2 MUTATED"        
clus
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               2               31 
      TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173       TCGA-B1-A654 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-7268       TCGA-B9-A44B 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-B9-A69E       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-DW-7963       TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-A59T       TCGA-HE-A5NI       TCGA-HE-A5NJ 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-HE-A5NK       TCGA-IA-A40U       TCGA-IZ-A6M8       TCGA-P4-A5E7 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-P4-A5EB       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
D14V10, continuous
[1] "Remove cluster labels:" "AHNAK2 MUTATED"        
clus
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               2               18 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-A69E 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-6793       TCGA-G7-6795 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-G7-7501       TCGA-HE-A5NI       TCGA-IA-A40U       TCGA-P4-A5E6 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHNAK2 MUTATED                                  1     0
  AHNAK2 WILD-TYPE                                1     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AHNAK2 MUTATED                           1     3
  AHNAK2 WILD-TYPE                        41    99
D14V11, multiclass
                                  clus
vv                                 AHNAK2 MUTATED AHNAK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     1               41
  WHITE                                         3               99
[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
  AHNAK2 MUTATED     0   4
  AHNAK2 WILD-TYPE   6 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED      0    4
  AHNAK2 WILD-TYPE    6  117
                        clus
vv                       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              117
[1] 2 2
[1] FALSE

Clustering(15) Variable = OR2L8 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  OR2L8 MUTATED     2   2
  OR2L8 WILD-TYPE 134  20
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              4             154 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              2              20 
$`OR2L8 MUTATED`
TCGA-BQ-5889 TCGA-DZ-6133 TCGA-EV-5903 TCGA-IZ-8196 
       10.82        51.19        24.89        21.34 

$`OR2L8 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       66.71        62.66        67.73         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6789 
       61.02        74.60        34.19        19.00        10.68         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-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       20.52        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        84.89        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-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
        2.04        22.26        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  OR2L8 MUTATED OR2L8 WILD-TYPE 
          10.82            0.10 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
          51.19          194.79 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
         23.115          20.840 
[1] "10.8 - 51.2 (23.1)" "0.1 - 194.8 (20.8)"
[1] "hr=" "3.3"
D15V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OR2L8 MUTATED         3        0         0        1
  OR2L8 WILD-TYPE      93        8        36        9
D15V3, multiclass
           clus
vv          OR2L8 MUTATED OR2L8 WILD-TYPE
  STAGE I               3              93
  STAGE II              0               8
  STAGE III             0              36
  STAGE IV              1               9
[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
  OR2L8 MUTATED     3   0     1
  OR2L8 WILD-TYPE 100  16    41
D15V4, multiclass
       clus
vv      OR2L8 MUTATED OR2L8 WILD-TYPE
  T1                3             100
  T2                0              16
  T3+T4             1              41
[1] 3 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
  OR2L8 MUTATED    0  1  0
  OR2L8 WILD-TYPE 28 16  4
D15V5, multiclass
[1] "Remove cluster labels:" "OR2L8 MUTATED"         
clus
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              1              48 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B1-A657      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5890      TCGA-BQ-5891 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
D15V6, binary
                 cls
clus               0  1
  OR2L8 MUTATED    1  1
  OR2L8 WILD-TYPE 62  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      1    1
  OR2L8 WILD-TYPE   62    5
   clus
vv  OR2L8 MUTATED OR2L8 WILD-TYPE
  0             1              62
  1             1               5
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus                0   1
  OR2L8 MUTATED     1   3
  OR2L8 WILD-TYPE  46 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      1    3
  OR2L8 WILD-TYPE   46  111
        clus
vv       OR2L8 MUTATED OR2L8 WILD-TYPE
  FEMALE             1              46
  MALE               3             111
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:" "OR2L8 MUTATED"         
clus
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              1              43 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
D15V9, continuous
D15V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2L8 MUTATED                                  0     0
  OR2L8 WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2L8 MUTATED                           0     4
  OR2L8 WILD-TYPE                        42    98
D15V11, multiclass
                                  clus
vv                                 OR2L8 MUTATED OR2L8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    0              42
  WHITE                                        4              98
[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
  OR2L8 MUTATED     0   3
  OR2L8 WILD-TYPE   6 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      0    3
  OR2L8 WILD-TYPE    6  118
                        clus
vv                       OR2L8 MUTATED OR2L8 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             118
[1] 2 2
[1] FALSE

Clustering(16) Variable = PAM MUTATION ANALYSIS
D16V1, survival
               sevent
clus2             0   1
  PAM MUTATED     3   0
  PAM WILD-TYPE 133  22
  PAM MUTATED PAM WILD-TYPE 
            3           155 
  PAM MUTATED PAM WILD-TYPE 
            0            22 
$`PAM MUTATED`
TCGA-HE-A5NI TCGA-IA-A40U TCGA-P4-A5E6 
       11.84        16.80        99.78 

$`PAM WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       66.71        62.66        67.73         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         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         6.38 
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-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       17.95        84.89        26.01        56.75        73.25        25.22 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       30.38        27.65        20.25        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       99.12        92.58        19.73        17.75        14.07 

  PAM MUTATED PAM WILD-TYPE 
        11.84          0.10 
  PAM MUTATED PAM WILD-TYPE 
        99.78        194.79 
  PAM MUTATED PAM WILD-TYPE 
        16.80         21.34 
[1] "11.8 - 99.8 (16.8)" "0.1 - 194.8 (21.3)"
[1] "hr="     "9200000"
D16V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  PAM MUTATED         1        0         2        0
  PAM WILD-TYPE      95        8        34       10
D16V3, multiclass
           clus
vv          PAM MUTATED PAM WILD-TYPE
  STAGE I             1            95
  STAGE II            0             8
  STAGE III           2            34
  STAGE IV            0            10
[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 101  16    41
D16V4, multiclass
       clus
vv      PAM MUTATED PAM WILD-TYPE
  T1              2           101
  T2              0            16
  T3+T4           1            41
[1] 3 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  0
  PAM WILD-TYPE 27 16  4
D16V5, multiclass
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2            47 
   TCGA-A4-7583    TCGA-A4-7585    TCGA-A4-7915    TCGA-A4-A57E    TCGA-A4-A5Y1 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173    TCGA-B1-5398 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A655    TCGA-B1-A656    TCGA-B1-A657    TCGA-B9-7268    TCGA-BQ-5877 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880    TCGA-BQ-5882    TCGA-BQ-5885 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890    TCGA-BQ-5891 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7045    TCGA-BQ-7048 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7058    TCGA-DW-7963    TCGA-DZ-6131 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6789    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-6846 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-7966    TCGA-GL-A59R    TCGA-IA-A40Y    TCGA-J7-6720    TCGA-J7-8537 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-P4-A5E8    TCGA-P4-A5EA 
"PAM WILD-TYPE" "PAM WILD-TYPE" 
D16V6, binary
               cls
clus             0  1
  PAM MUTATED    1  0
  PAM WILD-TYPE 62  6
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      1    0
  PAM WILD-TYPE   62    6
   clus
vv  PAM MUTATED PAM WILD-TYPE
  0           1            62
  1           0             6
[1] 2 2
[1] FALSE
D16V7, binary
               cls
clus              0   1
  PAM MUTATED     0   3
  PAM WILD-TYPE  47 111
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    3
  PAM WILD-TYPE   47  111
        clus
vv       PAM MUTATED PAM WILD-TYPE
  FEMALE           0            47
  MALE             3           111
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            1            43 
   TCGA-A4-7286    TCGA-A4-7828    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-A4-8517    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A48D 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU    TCGA-A4-A5XZ    TCGA-A4-A6HP 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6797    TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40X 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IA-A40Y    TCGA-J7-8537    TCGA-Q2-A5QZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
D16V9, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2            31 
   TCGA-A4-8310    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4115 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-7268    TCGA-B9-A44B    TCGA-B9-A69E    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-DW-7963    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-GL-7773    TCGA-GL-A59T    TCGA-HE-A5NJ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-HE-A5NK    TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Q2-A5QZ 
"PAM WILD-TYPE" 
D16V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAM MUTATED                                  0     0
  PAM WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PAM MUTATED                           1     1
  PAM WILD-TYPE                        41   101
D16V11, multiclass
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2           146 
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7584 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7585    TCGA-A4-7732    TCGA-A4-7734    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-A5Y1    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-AL-3467 
"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-AT-A5NU    TCGA-B1-5398 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A47M    TCGA-B1-A47N    TCGA-B1-A654    TCGA-B1-A655    TCGA-B1-A656 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A657    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-B9-5156    TCGA-B9-7268    TCGA-B9-A44B    TCGA-B9-A5W7 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A5W8    TCGA-B9-A5W9    TCGA-B9-A69E    TCGA-BQ-5875    TCGA-BQ-5876 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880    TCGA-BQ-5881 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5883    TCGA-BQ-5884    TCGA-BQ-5885    TCGA-BQ-5886    TCGA-BQ-5887 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5893    TCGA-BQ-7044    TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7058 
"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-5560 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    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-DW-7963    TCGA-DZ-6131 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DZ-6133    TCGA-DZ-6134    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-G7-6789    TCGA-G7-6790    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-G7-6796    TCGA-G7-6797    TCGA-G7-7501    TCGA-G7-7502 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-A4TM    TCGA-GL-6846    TCGA-GL-7773    TCGA-GL-7966    TCGA-GL-8500 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-A4EM    TCGA-GL-A59R    TCGA-GL-A59T    TCGA-IA-A40X    TCGA-IA-A40Y 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IZ-8195    TCGA-IZ-8196    TCGA-IZ-A6M8    TCGA-IZ-A6M9    TCGA-J7-6720 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-J7-8537    TCGA-KV-A6GD    TCGA-KV-A6GE    TCGA-MH-A55W    TCGA-MH-A55Z 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-MH-A560    TCGA-MH-A561    TCGA-MH-A562    TCGA-P4-A5E7    TCGA-P4-A5E8 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-P4-A5EA    TCGA-P4-A5EB    TCGA-P4-A5ED    TCGA-PJ-A5Z8    TCGA-PJ-A5Z9 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Q2-A5QZ 
"PAM WILD-TYPE" 
D16V12, binary
               cls
clus              0   1
  PAM MUTATED     0   2
  PAM WILD-TYPE   6 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    2
  PAM WILD-TYPE    6  119
                        clus
vv                       PAM MUTATED PAM WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           2           119
[1] 2 2
[1] FALSE

Clustering(17) Variable = IDUA MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  IDUA MUTATED     4   1
  IDUA WILD-TYPE 132  21
  IDUA MUTATED IDUA WILD-TYPE 
             5            153 
  IDUA MUTATED IDUA WILD-TYPE 
             1             21 
$`IDUA MUTATED`
TCGA-A4-7585 TCGA-BQ-5883 TCGA-G7-6792 TCGA-GL-7773 TCGA-P4-A5EB 
       35.18        40.83        90.90        12.92        99.12 

$`IDUA WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        21.37        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        51.78        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       20.52        25.84         6.38       194.79         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        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-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       20.25        99.78        87.09        42.94         6.61        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  IDUA MUTATED IDUA WILD-TYPE 
         12.92           0.10 
  IDUA MUTATED IDUA WILD-TYPE 
         99.12         194.79 
  IDUA MUTATED IDUA WILD-TYPE 
         40.83          20.61 
[1] "12.9 - 99.1 (40.8)" "0.1 - 194.8 (20.6)"
[1] "hr=" "1.1"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IDUA MUTATED         4        0         1        0
  IDUA WILD-TYPE      92        8        35       10
D17V3, multiclass
           clus
vv          IDUA MUTATED IDUA WILD-TYPE
  STAGE I              4             92
  STAGE II             0              8
  STAGE III            1             35
  STAGE IV             0             10
[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
  IDUA MUTATED    4  0     1
  IDUA WILD-TYPE 99 16    41
D17V4, multiclass
       clus
vv      IDUA MUTATED IDUA WILD-TYPE
  T1               4             99
  T2               0             16
  T3+T4            1             41
[1] 3 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
  IDUA MUTATED    1  0  0
  IDUA WILD-TYPE 27 17  4
D17V5, multiclass
[1] "Remove cluster labels:" "IDUA MUTATED"          
clus
  IDUA MUTATED IDUA WILD-TYPE 
             1             48 
    TCGA-A4-7583     TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A5Y1 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656     TCGA-B1-A657 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7058 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
D17V6, binary
                cls
clus              0  1
  IDUA MUTATED    2  0
  IDUA WILD-TYPE 61  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      2    0
  IDUA WILD-TYPE   61    6
   clus
vv  IDUA MUTATED IDUA WILD-TYPE
  0            2             61
  1            0              6
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus               0   1
  IDUA MUTATED     1   4
  IDUA WILD-TYPE  46 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      1    4
  IDUA WILD-TYPE   46  110
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  FEMALE            1             46
  MALE              4            110
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "IDUA MUTATED"          
clus
  IDUA MUTATED IDUA WILD-TYPE 
             1             43 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098     TCGA-A4-8310 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8517     TCGA-A4-8518 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-A4-8630     TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6793 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-G7-7502     TCGA-G7-A4TM     TCGA-IA-A40U     TCGA-IA-A40X 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-8537     TCGA-Q2-A5QZ 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
D17V9, continuous
D17V10, continuous
[1] "Remove cluster labels:" "IDUA MUTATED"          
clus
  IDUA MUTATED IDUA WILD-TYPE 
             1             19 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-6793 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-HE-A5NI     TCGA-IA-A40U 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDUA MUTATED                                  0     0
  IDUA WILD-TYPE                                2     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDUA MUTATED                           2     3
  IDUA WILD-TYPE                        40    99
D17V11, multiclass
                                  clus
vv                                 IDUA MUTATED IDUA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   2             40
  WHITE                                       3             99
[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
  IDUA MUTATED     0   4
  IDUA WILD-TYPE   6 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      0    4
  IDUA WILD-TYPE    6  117
                        clus
vv                       IDUA MUTATED IDUA WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            117
[1] 2 2
[1] FALSE

Clustering(18) Variable = CSGALNACT2 MUTATION ANALYSIS
D18V1, survival
                      sevent
clus2                    0   1
  CSGALNACT2 MUTATED     4   0
  CSGALNACT2 WILD-TYPE 132  22
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   4                  154 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   0                   22 
$`CSGALNACT2 MUTATED`
TCGA-A4-A4ZT TCGA-HE-A5NK TCGA-KV-A6GD TCGA-MH-A560 
       16.96        73.25        18.41        30.38 

$`CSGALNACT2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         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-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       84.89        26.01        11.84        56.75        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 
       12.76        10.55        29.10        34.29        27.78        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               16.96                 0.10 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               73.25               194.79 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
              24.395               21.205 
[1] "17.0 - 73.2 (24.4)" "0.1 - 194.8 (21.2)"
[1] "hr="     "2.5e+07"
D18V2, continuous
                      vv
clus                   STAGE I STAGE II STAGE III STAGE IV
  CSGALNACT2 MUTATED         3        0         1        0
  CSGALNACT2 WILD-TYPE      93        8        35       10
D18V3, multiclass
           clus
vv          CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  STAGE I                    3                   93
  STAGE II                   0                    8
  STAGE III                  1                   35
  STAGE IV                   0                   10
[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
  CSGALNACT2 MUTATED    4  0     1
  CSGALNACT2 WILD-TYPE 99 16    41
D18V4, multiclass
       clus
vv      CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  T1                     4                   99
  T2                     0                   16
  T3+T4                  1                   41
[1] 3 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
  CSGALNACT2 MUTATED    0  0  0
  CSGALNACT2 WILD-TYPE 28 17  4
D18V5, multiclass
D18V6, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    3  0
  CSGALNACT2 WILD-TYPE 60  6
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    0
  CSGALNACT2 WILD-TYPE   60    6
   clus
vv  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  0                  3                   60
  1                  0                    6
[1] 2 2
[1] FALSE
D18V7, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     2   3
  CSGALNACT2 WILD-TYPE  45 111
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      2    3
  CSGALNACT2 WILD-TYPE   45  111
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  FEMALE                  2                   45
  MALE                    3                  111
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   43 
          TCGA-A4-7286           TCGA-A4-7828           TCGA-A4-8098 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-8310           TCGA-A4-8311           TCGA-A4-8312 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-8517           TCGA-A4-8518           TCGA-A4-8630 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-A48D           TCGA-A4-A57E           TCGA-A4-A5DU 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-A5XZ           TCGA-A4-A6HP           TCGA-AL-3466 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-5560           TCGA-DW-5561           TCGA-DW-7834 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7837           TCGA-DW-7838           TCGA-DW-7839 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7840           TCGA-DW-7841           TCGA-DW-7842 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7963           TCGA-EV-5901           TCGA-EV-5902 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-EV-5903           TCGA-G7-6789           TCGA-G7-6790 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-6792           TCGA-G7-6793           TCGA-G7-6795 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-6796           TCGA-G7-6797           TCGA-G7-7501 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-7502           TCGA-G7-A4TM           TCGA-IA-A40U 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-IA-A40X           TCGA-IA-A40Y           TCGA-J7-8537 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-Q2-A5QZ 
"CSGALNACT2 WILD-TYPE" 
D18V9, continuous
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   32 
          TCGA-A4-8310           TCGA-A4-A48D           TCGA-A4-A57E 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-A5Y0           TCGA-AL-3466           TCGA-AL-3472 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-AL-7173           TCGA-B1-A654           TCGA-B9-4114 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B9-4115           TCGA-B9-4117           TCGA-B9-7268 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B9-A44B           TCGA-B9-A69E           TCGA-DW-5561 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7834           TCGA-DW-7838           TCGA-DW-7963 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-6792           TCGA-G7-6793           TCGA-G7-6795 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-7501           TCGA-GL-7773           TCGA-GL-A59T 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-HE-A5NI           TCGA-HE-A5NJ           TCGA-IA-A40U 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-IZ-A6M8           TCGA-P4-A5E7           TCGA-P4-A5EB 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-PJ-A5Z9           TCGA-Q2-A5QZ 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
D18V10, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSGALNACT2 MUTATED                                  0     0
  CSGALNACT2 WILD-TYPE                                2     2
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  CSGALNACT2 MUTATED                           0     3
  CSGALNACT2 WILD-TYPE                        42    99
D18V11, multiclass
                                  clus
vv                                 CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    2
  ASIAN                                             0                    2
  BLACK OR AFRICAN AMERICAN                         0                   42
  WHITE                                             3                   99
[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
  CSGALNACT2 MUTATED     0   3
  CSGALNACT2 WILD-TYPE   6 118
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      0    3
  CSGALNACT2 WILD-TYPE    6  118
                        clus
vv                       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  HISPANIC OR LATINO                      0                    6
  NOT HISPANIC OR LATINO                  3                  118
[1] 2 2
[1] FALSE

Clustering(19) Variable = RPL7A MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  RPL7A MUTATED     2   1
  RPL7A WILD-TYPE 134  21
  RPL7A MUTATED RPL7A WILD-TYPE 
              3             155 
  RPL7A MUTATED RPL7A WILD-TYPE 
              1              21 
$`RPL7A MUTATED`
TCGA-BQ-5889 TCGA-DW-7841 TCGA-P4-A5EB 
       10.82        14.63        99.12 

$`RPL7A WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       66.71        62.66        67.73         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
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-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
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-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        92.58        19.73        17.75        14.07 

  RPL7A MUTATED RPL7A WILD-TYPE 
          10.82            0.10 
  RPL7A MUTATED RPL7A WILD-TYPE 
          99.12          194.79 
  RPL7A MUTATED RPL7A WILD-TYPE 
          14.63           21.34 
[1] "10.8 - 99.1 (14.6)" "0.1 - 194.8 (21.3)"
[1] "hr=" "2.1"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RPL7A MUTATED         2        0         0        1
  RPL7A WILD-TYPE      94        8        36        9
D19V3, multiclass
           clus
vv          RPL7A MUTATED RPL7A WILD-TYPE
  STAGE I               2              94
  STAGE II              0               8
  STAGE III             0              36
  STAGE IV              1               9
[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
  RPL7A MUTATED     2   0     1
  RPL7A WILD-TYPE 101  16    41
D19V4, multiclass
       clus
vv      RPL7A MUTATED RPL7A WILD-TYPE
  T1                2             101
  T2                0              16
  T3+T4             1              41
[1] 3 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
  RPL7A MUTATED    0  1  0
  RPL7A WILD-TYPE 28 16  4
D19V5, multiclass
[1] "Remove cluster labels:" "RPL7A MUTATED"         
clus
  RPL7A MUTATED RPL7A WILD-TYPE 
              1              48 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B1-A657      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5890      TCGA-BQ-5891 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
D19V6, binary
                 cls
clus               0  1
  RPL7A MUTATED    0  1
  RPL7A WILD-TYPE 63  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL7A MUTATED      0    1
  RPL7A WILD-TYPE   63    5
   clus
vv  RPL7A MUTATED RPL7A WILD-TYPE
  0             0              63
  1             1               5
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  RPL7A MUTATED     0   3
  RPL7A WILD-TYPE  47 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL7A MUTATED      0    3
  RPL7A WILD-TYPE   47  111
        clus
vv       RPL7A MUTATED RPL7A WILD-TYPE
  FEMALE             0              47
  MALE               3             111
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "RPL7A MUTATED"         
clus
  RPL7A MUTATED RPL7A WILD-TYPE 
              1              43 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7842 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
D19V9, continuous
[1] "Remove cluster labels:" "RPL7A MUTATED"         
clus
  RPL7A MUTATED RPL7A WILD-TYPE 
              1              32 
     TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173      TCGA-B1-A654 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4117      TCGA-B9-7268 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7963      TCGA-G7-6792      TCGA-G7-6793 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
D19V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPL7A MUTATED                                  0     0
  RPL7A WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RPL7A MUTATED                           1     2
  RPL7A WILD-TYPE                        41   100
D19V11, multiclass
                                  clus
vv                                 RPL7A MUTATED RPL7A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    1              41
  WHITE                                        2             100
[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
  RPL7A MUTATED     0   3
  RPL7A WILD-TYPE   6 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL7A MUTATED      0    3
  RPL7A WILD-TYPE    6  118
                        clus
vv                       RPL7A MUTATED RPL7A WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             118
[1] 2 2
[1] FALSE
