[1] "ofn"       "-oTUCS-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/UCS-TP/22507158/UCS-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/22569432/transformed.cor.cli.txt"

nPatients in clinical file=57, in cluster file=57, common to both=57
[1] "Reduce the number of clustering variables from 12 to 11."
[1] 11 57
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            51              6 
  TP53 MUTATED TP53 WILD-TYPE 
            51              6 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             22              35 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             22              35 
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               16                41 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               16                41 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             7             50 
  KRAS MUTATED KRAS WILD-TYPE 
             7             50 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            11             46 
  PTEN MUTATED PTEN WILD-TYPE 
            11             46 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            6            51 
  RB1 MUTATED RB1 WILD-TYPE 
            6            51 
[1] "ZBTB7B MUTATION ANALYSIS"
[1] 3
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               6               51 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               6               51 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               6               51 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               6               51 
[1] "ARHGAP35 MUTATION ANALYSIS"
[1] 3
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 6                 51 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 6                 51 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              20               37 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              20               37 
[1] "MAMLD1 MUTATION ANALYSIS"
[1] 3
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               4               53 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               4               53 
[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] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RACE"                                
[15] "ETHNICITY"                           

Input Data has 15 rows and 57 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=34,	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=22,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "43"                  
freq.contrast "43"               "1"                   
both >= 3     "FALSE"            "FALSE"               
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 57 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "RADIATION_THERAPY" "HISTOLOGICAL_TYPE"
[4] "RACE"             
YEARS_TO_BIRTH, nv=30, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   21 29
  TP53 WILD-TYPE  0  6
  TP53 MUTATED TP53 WILD-TYPE 
            50              6 
  TP53 MUTATED TP53 WILD-TYPE 
            29              6 
$`TP53 MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       34.62        81.70         9.57        27.25        20.09        25.18 
TCGA-QM-A5NM TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ 
       19.30       102.41        52.31         4.67        59.38        18.08 
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
        4.87        22.52        29.95        50.17        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 
       11.87        32.19        19.63        17.16        51.75         0.26 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ 
       27.19        26.63        13.74        26.70        25.68        18.81 
TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       12.20        21.93        67.17        54.97        35.80        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 
       15.81       140.35        80.78        27.55         3.75        17.79 
TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
        6.67        10.42         9.80        14.86         2.66         5.49 
TCGA-NG-A4VU TCGA-N7-A4Y8 
       14.53        12.43 

$`TP53 WILD-TYPE`
TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NG-A4VW 
        3.68        25.35        88.11        23.47         5.49        31.20 

  TP53 MUTATED TP53 WILD-TYPE 
          0.26           3.68 
  TP53 MUTATED TP53 WILD-TYPE 
        140.35          88.11 
  TP53 MUTATED TP53 WILD-TYPE 
        19.975         24.410 
[1] "0.3 - 140.3 (20.0)" "3.7 - 88.1 (24.4)" 
[1] "hr=" "1.6"
D1V2, continuous
D1V3, binary
                cls
clus              0  1
  TP53 MUTATED   27 21
  TP53 WILD-TYPE  2  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     27   21
  TP53 WILD-TYPE    2    4
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            27              2
  YES           21              4
[1] 2 2
[1] FALSE
                vv
clus             UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  TP53 MUTATED                                                                    21
  TP53 WILD-TYPE                                                                   3
                vv
clus             UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  TP53 MUTATED                                                17
  TP53 WILD-TYPE                                               3
                vv
clus             UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  TP53 MUTATED                                             13
  TP53 WILD-TYPE                                            0
D1V4, multiclass
                                                                     clus
vv                                                                    TP53 MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS           21
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                               17
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                  13
                                                                     clus
vv                                                                    TP53 WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  3
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                     0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       2                         9    39
  TP53 WILD-TYPE     1                         0     5
D1V5, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                2              1
  BLACK OR AFRICAN AMERICAN            9              0
  WHITE                               39              5
[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"

Clustering(2) Variable = FBXW7 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED    8 14
  FBXW7 WILD-TYPE 13 21
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             22              34 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             14              21 
$`FBXW7 MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-ND-A4WC 
       34.62        81.70         3.68         9.57        27.25        25.18 
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A59F 
       52.31         4.67        18.08        22.52        29.95        11.87 
TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N8-A4PI TCGA-N8-A4PN TCGA-N9-A4Q7 TCGA-NA-A4QX 
       19.63        51.75        26.63        26.70        19.86        27.55 
TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NG-A4VU TCGA-N7-A4Y8 
        5.49        14.86        14.53        12.43 

$`FBXW7 WILD-TYPE`
TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4R8 TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RU 
       20.09        19.30       102.41        59.38         4.87        50.17 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       67.13        14.70        32.19        17.16        25.35         0.26 
TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       27.19        13.74        25.68        18.81        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       67.17        54.97        35.80        15.81       140.35        80.78 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
        3.75        17.79         6.67        88.11        10.42        23.47 
TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW 
        9.80         2.66         5.49        31.20 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           3.68            0.26 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          81.70          140.35 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          21.19           21.01 
[1] "3.7 - 81.7 (21.2)"  "0.3 - 140.3 (21.0)"
[1] "hr=" "1.3"
D2V2, continuous
D2V3, binary
                 cls
clus               0  1
  FBXW7 MUTATED   10 11
  FBXW7 WILD-TYPE 19 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     10   11
  FBXW7 WILD-TYPE   19   14
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             10              19
  YES            11              14
[1] 2 2
[1] FALSE
                 vv
clus              UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  FBXW7 MUTATED                                                                     7
  FBXW7 WILD-TYPE                                                                  17
                 vv
clus              UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  FBXW7 MUTATED                                                 7
  FBXW7 WILD-TYPE                                              13
                 vv
clus              UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  FBXW7 MUTATED                                              8
  FBXW7 WILD-TYPE                                            5
D2V4, multiclass
                                                                     clus
vv                                                                    FBXW7 MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS             7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                 7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                    8
                                                                     clus
vv                                                                    FBXW7 WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  13
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       1                         3    17
  FBXW7 WILD-TYPE     2                         6    27
D2V5, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 1               2
  BLACK OR AFRICAN AMERICAN             3               6
  WHITE                                17              27
[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"

Clustering(3) Variable = PPP2R1A MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  PPP2R1A MUTATED    8  8
  PPP2R1A WILD-TYPE 13 27
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               16                40 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
                8                27 
$`PPP2R1A MUTATED`
TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RF TCGA-N5-A4RU 
        3.68        20.09        25.18        19.30        59.38        50.17 
TCGA-N5-A59E TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4QW 
       14.70        13.74        26.70        54.97        19.86        80.78 
TCGA-NA-A4QX TCGA-ND-A4WF TCGA-NF-A4X2 TCGA-NG-A4VU 
       27.55         5.49         2.66        14.53 

$`PPP2R1A WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N5-A4R8 TCGA-N5-A4RA 
       34.62        81.70         9.57        27.25       102.41        52.31 
TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RV 
        4.67        18.08         4.87        22.52        29.95        67.13 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       11.87        32.19        19.63        17.16        51.75        25.35 
TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S 
        0.26        27.19        26.63        25.68        18.81        12.20 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QY 
       21.93        67.17        35.80        15.81       140.35         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU 
       17.79         6.67        88.11        10.42        23.47         9.80 
TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VW TCGA-N7-A4Y8 
       14.86         5.49        31.20        12.43 

  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
             2.66              0.26 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
            80.78            140.35 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           19.975            22.225 
[1] "2.7 - 80.8 (20.0)"  "0.3 - 140.3 (22.2)"
[1] "hr=" "1.2"
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  PPP2R1A MUTATED    7  9
  PPP2R1A WILD-TYPE 22 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED      7    9
  PPP2R1A WILD-TYPE   22   16
     clus
vv    PPP2R1A MUTATED PPP2R1A WILD-TYPE
  NO                7                22
  YES               9                16
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  PPP2R1A MUTATED                                                                     8
  PPP2R1A WILD-TYPE                                                                  16
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  PPP2R1A MUTATED                                                 3
  PPP2R1A WILD-TYPE                                              17
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  PPP2R1A MUTATED                                              5
  PPP2R1A WILD-TYPE                                            8
D3V4, multiclass
                                                                     clus
vv                                                                    PPP2R1A MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               8
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   3
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      5
                                                                     clus
vv                                                                    PPP2R1A WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                16
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    17
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP2R1A MUTATED       1                         1    14
  PPP2R1A WILD-TYPE     2                         8    30
D3V5, multiclass
                           clus
vv                          PPP2R1A MUTATED PPP2R1A WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 8
  WHITE                                  14                30
[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"

Clustering(4) Variable = KRAS MUTATION ANALYSIS
D4V1, survival
                sevent
clus2             0  1
  KRAS MUTATED    4  3
  KRAS WILD-TYPE 17 32
  KRAS MUTATED KRAS WILD-TYPE 
             7             49 
  KRAS MUTATED KRAS WILD-TYPE 
             3             32 
$`KRAS MUTATED`
TCGA-N5-A4RF TCGA-N5-A4RS TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N8-A4PL TCGA-N9-A4Q3 
       59.38        29.95        32.19        19.63        13.74        54.97 
TCGA-NF-A4WU 
        9.80 

$`KRAS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP 
       34.62        81.70         3.68         9.57        27.25        20.09 
TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ 
       25.18        19.30       102.41        52.31         4.67        18.08 
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
        4.87        22.52        50.17        67.13        14.70        11.87 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI 
       17.16        51.75        25.35         0.26        27.19        26.63 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       26.70        25.68        18.81        12.20        21.93        67.17 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       35.80        19.86        15.81       140.35        80.78        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
        3.75        17.79         6.67        88.11        10.42        23.47 
TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        5.49        14.86         2.66         5.49        14.53        31.20 
TCGA-N7-A4Y8 
       12.43 

  KRAS MUTATED KRAS WILD-TYPE 
          9.80           0.26 
  KRAS MUTATED KRAS WILD-TYPE 
         59.38         140.35 
  KRAS MUTATED KRAS WILD-TYPE 
         29.95          20.09 
[1] "9.8 - 59.4 (29.9)"  "0.3 - 140.3 (20.1)"
[1] "hr=" "1.7"
D4V2, continuous
D4V3, binary
                cls
clus              0  1
  KRAS MUTATED    3  4
  KRAS WILD-TYPE 26 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      3    4
  KRAS WILD-TYPE   26   21
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             3             26
  YES            4             21
[1] 2 2
[1] FALSE
                vv
clus             UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  KRAS MUTATED                                                                     5
  KRAS WILD-TYPE                                                                  19
                vv
clus             UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  KRAS MUTATED                                                 0
  KRAS WILD-TYPE                                              20
                vv
clus             UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  KRAS MUTATED                                              2
  KRAS WILD-TYPE                                           11
D4V4, multiclass
                                                                     clus
vv                                                                    KRAS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS            5
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                0
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                   2
                                                                     clus
vv                                                                    KRAS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS             19
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                 20
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                    11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0     7
  KRAS WILD-TYPE     3                         9    37
D4V5, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              9
  WHITE                                7             37
[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"

Clustering(5) Variable = PTEN MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  PTEN MUTATED    4  7
  PTEN WILD-TYPE 17 28
  PTEN MUTATED PTEN WILD-TYPE 
            11             45 
  PTEN MUTATED PTEN WILD-TYPE 
             7             28 
$`PTEN MUTATED`
TCGA-N6-A4VD TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RF TCGA-N6-A4VF TCGA-N7-A4Y0 
        3.68        25.18        19.30        59.38        17.16        25.35 
TCGA-N8-A4PI TCGA-NA-A4R1 TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW 
       26.63         6.67         2.66         5.49        31.20 

$`PTEN WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N5-A4R8 
       34.62        81.70         9.57        27.25        20.09       102.41 
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS 
       52.31         4.67        18.08         4.87        22.52        29.95 
TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       50.17        67.13        14.70        11.87        32.19        19.63 
TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO 
       51.75         0.26        27.19        13.74        26.70        25.68 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       18.81        12.20        21.93        67.17        54.97        35.80 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY 
       19.86        15.81       140.35        80.78        27.55         3.75 
TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU 
       17.79        88.11        10.42        23.47         5.49         9.80 
TCGA-NF-A4WX TCGA-NG-A4VU TCGA-N7-A4Y8 
       14.86        14.53        12.43 

  PTEN MUTATED PTEN WILD-TYPE 
          2.66           0.26 
  PTEN MUTATED PTEN WILD-TYPE 
         59.38         140.35 
  PTEN MUTATED PTEN WILD-TYPE 
         19.30          21.93 
[1] "2.7 - 59.4 (19.3)"  "0.3 - 140.3 (21.9)"
[1] "hr=" "1.4"
D5V2, continuous
D5V3, binary
                cls
clus              0  1
  PTEN MUTATED    5  6
  PTEN WILD-TYPE 24 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    6
  PTEN WILD-TYPE   24   19
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             5             24
  YES            6             19
[1] 2 2
[1] FALSE
                vv
clus             UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  PTEN MUTATED                                                                     6
  PTEN WILD-TYPE                                                                  18
                vv
clus             UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  PTEN MUTATED                                                 3
  PTEN WILD-TYPE                                              17
                vv
clus             UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  PTEN MUTATED                                              2
  PTEN WILD-TYPE                                           11
D5V4, multiclass
                                                                     clus
vv                                                                    PTEN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS            6
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                3
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                   2
                                                                     clus
vv                                                                    PTEN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS             18
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                 17
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                    11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       1                         1     9
  PTEN WILD-TYPE     2                         8    35
D5V5, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            1              8
  WHITE                                9             35
[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"

Clustering(6) Variable = RB1 MUTATION ANALYSIS
D6V1, survival
               sevent
clus2            0  1
  RB1 MUTATED    4  2
  RB1 WILD-TYPE 17 33
  RB1 MUTATED RB1 WILD-TYPE 
            6            50 
  RB1 MUTATED RB1 WILD-TYPE 
            2            33 
$`RB1 MUTATED`
TCGA-N5-A4RN TCGA-ND-A4WC TCGA-N5-A4RF TCGA-N5-A4RV TCGA-NA-A4R1 TCGA-NG-A4VW 
       34.62        25.18        59.38        67.13         6.67        31.20 

$`RB1 WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-QM-A5NM 
       81.70         3.68         9.57        27.25        20.09        19.30 
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
      102.41        52.31         4.67        18.08         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       29.95        50.17        14.70        11.87        32.19        19.63 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI 
       17.16        51.75        25.35         0.26        27.19        26.63 
TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       13.74        26.70        25.68        18.81        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV 
       67.17        54.97        35.80        19.86        15.81       140.35 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 
       80.78        27.55         3.75        17.79        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       23.47         5.49         9.80        14.86         2.66         5.49 
TCGA-NG-A4VU TCGA-N7-A4Y8 
       14.53        12.43 

  RB1 MUTATED RB1 WILD-TYPE 
         6.67          0.26 
  RB1 MUTATED RB1 WILD-TYPE 
        67.13        140.35 
  RB1 MUTATED RB1 WILD-TYPE 
       32.910        19.745 
[1] "6.7 - 67.1 (32.9)"  "0.3 - 140.3 (19.7)"
[1] "hr=" "2.6"
D6V2, continuous
D6V3, binary
               cls
clus             0  1
  RB1 MUTATED    1  5
  RB1 WILD-TYPE 28 20
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1    5
  RB1 WILD-TYPE   28   20
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            1            28
  YES           5            20
[1] 2 2
[1] FALSE
               vv
clus            UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  RB1 MUTATED                                                                     2
  RB1 WILD-TYPE                                                                  22
               vv
clus            UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  RB1 MUTATED                                                 0
  RB1 WILD-TYPE                                              20
               vv
clus            UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  RB1 MUTATED                                              4
  RB1 WILD-TYPE                                            9
D6V4, multiclass
                                                                     clus
vv                                                                    RB1 MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS           2
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                               0
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                  4
                                                                     clus
vv                                                                    RB1 WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS            22
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                20
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                    9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       1                         1     4
  RB1 WILD-TYPE     2                         8    40
D6V5, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               1             2
  BLACK OR AFRICAN AMERICAN           1             8
  WHITE                               4            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"

Clustering(7) Variable = ZBTB7B MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  ZBTB7B MUTATED    2  3
  ZBTB7B WILD-TYPE 19 32
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               5               51 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               3               32 
$`ZBTB7B MUTATED`
TCGA-N5-A4RT TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N6-A4VG TCGA-NG-A4VW 
       81.70       102.41        52.31        51.75        31.20 

$`ZBTB7B WILD-TYPE`
TCGA-N5-A4RN TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       34.62         3.68         9.57        27.25        20.09        25.18 
TCGA-QM-A5NM TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
       19.30         4.67        59.38        18.08         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       29.95        50.17        67.13        14.70        11.87        32.19 
TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI 
       19.63        17.16        25.35         0.26        27.19        26.63 
TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       13.74        26.70        25.68        18.81        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV 
       67.17        54.97        35.80        19.86        15.81       140.35 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
       80.78        27.55         3.75        17.79         6.67        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 
       10.42        23.47         5.49         9.80        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
        5.49        14.53        12.43 

  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
           31.20             0.26 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
          102.41           140.35 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
           52.31            19.63 
[1] "31.2 - 102.4 (52.3)" "0.3 - 140.3 (19.6)" 
[1] "hr=" "2.4"
D7V2, continuous
D7V3, binary
                  cls
clus                0  1
  ZBTB7B MUTATED    2  4
  ZBTB7B WILD-TYPE 27 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7B MUTATED      2    4
  ZBTB7B WILD-TYPE   27   21
     clus
vv    ZBTB7B MUTATED ZBTB7B WILD-TYPE
  NO               2               27
  YES              4               21
[1] 2 2
[1] FALSE
                  vv
clus               UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  ZBTB7B MUTATED                                                                     3
  ZBTB7B WILD-TYPE                                                                  21
                  vv
clus               UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  ZBTB7B MUTATED                                                 2
  ZBTB7B WILD-TYPE                                              18
                  vv
clus               UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  ZBTB7B MUTATED                                              1
  ZBTB7B WILD-TYPE                                           12
D7V4, multiclass
                                                                     clus
vv                                                                    ZBTB7B MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  2
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                     1
                                                                     clus
vv                                                                    ZBTB7B WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               21
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   18
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB7B MUTATED       1                         0     5
  ZBTB7B WILD-TYPE     2                         9    39
D7V5, multiclass
                           clus
vv                          ZBTB7B MUTATED ZBTB7B WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                9
  WHITE                                  5               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"

Clustering(8) Variable = PIK3R1 MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2               0  1
  PIK3R1 MUTATED    1  4
  PIK3R1 WILD-TYPE 20 31
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               5               51 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               4               31 
$`PIK3R1 MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RS TCGA-N8-A4PI TCGA-N8-A4PN TCGA-NA-A4QX 
        4.67        29.95        26.63        26.70        27.55 

$`PIK3R1 WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP 
       34.62        81.70         3.68         9.57        27.25        20.09 
TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ 
       25.18        19.30       102.41        52.31        59.38        18.08 
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
        4.87        22.52        50.17        67.13        14.70        11.87 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       32.19        19.63        17.16        51.75        25.35         0.26 
TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       27.19        13.74        25.68        18.81        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV 
       67.17        54.97        35.80        19.86        15.81       140.35 
TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       80.78         3.75        17.79         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       23.47         5.49         9.80        14.86         2.66         5.49 
TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
       14.53        31.20        12.43 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            4.67             0.26 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           29.95           140.35 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           26.70            19.86 
[1] "4.7 - 29.9 (26.7)"  "0.3 - 140.3 (19.9)"
[1] "hr=" "1.3"
D8V2, continuous
D8V3, binary
                  cls
clus                0  1
  PIK3R1 MUTATED    2  3
  PIK3R1 WILD-TYPE 27 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      2    3
  PIK3R1 WILD-TYPE   27   22
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO               2               27
  YES              3               22
[1] 2 2
[1] FALSE
                  vv
clus               UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  PIK3R1 MUTATED                                                                     2
  PIK3R1 WILD-TYPE                                                                  22
                  vv
clus               UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  PIK3R1 MUTATED                                                 2
  PIK3R1 WILD-TYPE                                              18
                  vv
clus               UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  PIK3R1 MUTATED                                              2
  PIK3R1 WILD-TYPE                                           11
D8V4, multiclass
                                                                     clus
vv                                                                    PIK3R1 MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              2
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  2
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                     2
                                                                     clus
vv                                                                    PIK3R1 WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               22
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   18
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED       1                         0     5
  PIK3R1 WILD-TYPE     2                         9    39
D8V5, multiclass
                           clus
vv                          PIK3R1 MUTATED PIK3R1 WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                9
  WHITE                                  5               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"

Clustering(9) Variable = ARHGAP35 MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                 0  1
  ARHGAP35 MUTATED    2  4
  ARHGAP35 WILD-TYPE 19 31
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 6                 50 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 4                 31 
$`ARHGAP35 MUTATED`
TCGA-N8-A4PM TCGA-ND-A4WC TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-ND-A4WA TCGA-NG-A4VU 
       27.25        25.18        25.35         0.26        23.47        14.53 

$`ARHGAP35 WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PP TCGA-QM-A5NM 
       34.62        81.70         3.68         9.57        20.09        19.30 
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
      102.41        52.31         4.67        59.38        18.08         4.87 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
       22.52        29.95        50.17        67.13        14.70        11.87 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A59B TCGA-N8-A4PI 
       32.19        19.63        17.16        51.75        27.19        26.63 
TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       13.74        26.70        25.68        18.81        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV 
       67.17        54.97        35.80        19.86        15.81       140.35 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
       80.78        27.55         3.75        17.79         6.67        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       10.42         5.49         9.80        14.86         2.66         5.49 
TCGA-NG-A4VW TCGA-N7-A4Y8 
       31.20        12.43 

  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
              0.26               2.66 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
             27.25             140.35 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
            24.325             19.975 
[1] "0.3 - 27.2 (24.3)"  "2.7 - 140.3 (20.0)"
[1] "hr=" "1.4"
D9V2, continuous
D9V3, binary
                    cls
clus                  0  1
  ARHGAP35 MUTATED    4  2
  ARHGAP35 WILD-TYPE 25 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED      4    2
  ARHGAP35 WILD-TYPE   25   23
     clus
vv    ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  NO                 4                 25
  YES                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  ARHGAP35 MUTATED                                                                     1
  ARHGAP35 WILD-TYPE                                                                  23
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  ARHGAP35 MUTATED                                                 3
  ARHGAP35 WILD-TYPE                                              17
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  ARHGAP35 MUTATED                                              2
  ARHGAP35 WILD-TYPE                                           11
D9V4, multiclass
                                                                     clus
vv                                                                    ARHGAP35 MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                1
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    3
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       2
                                                                     clus
vv                                                                    ARHGAP35 WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 23
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     17
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP35 MUTATED       2                         0     4
  ARHGAP35 WILD-TYPE     1                         9    40
D9V5, multiclass
                           clus
vv                          ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                0                  9
  WHITE                                    4                 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"

Clustering(10) Variable = PIK3CA MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED    5 15
  PIK3CA WILD-TYPE 16 20
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              20               36 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              15               20 
$`PIK3CA MUTATED`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-ND-A4WC TCGA-N5-A4R8 TCGA-N5-A4RF 
       81.70         3.68        27.25        25.18       102.41        59.38 
TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N6-A4VF TCGA-N7-A4Y5 TCGA-N7-A59B 
       18.08        22.52        29.95        17.16         0.26        27.19 
TCGA-N9-A4PZ TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A5CP 
       21.93         3.75        17.79        10.42         5.49         5.49 
TCGA-NG-A4VW TCGA-N7-A4Y8 
       31.20        12.43 

$`PIK3CA WILD-TYPE`
TCGA-N5-A4RN TCGA-N6-A4VE TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD 
       34.62         9.57        20.09        19.30        52.31         4.67 
TCGA-N5-A4RM TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
        4.87        50.17        67.13        14.70        11.87        32.19 
TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN 
       19.63        51.75        25.35        26.63        13.74        26.70 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       25.68        18.81        12.20        67.17        54.97        35.80 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R1 
       19.86        15.81       140.35        80.78        27.55         6.67 
TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU 
       88.11        23.47         9.80        14.86         2.66        14.53 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.26             2.66 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          102.41           140.35 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          20.005           21.780 
[1] "0.3 - 102.4 (20.0)" "2.7 - 140.3 (21.8)"
[1] "hr=" "1.5"
D10V2, continuous
D10V3, binary
                  cls
clus                0  1
  PIK3CA MUTATED   10  9
  PIK3CA WILD-TYPE 19 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     10    9
  PIK3CA WILD-TYPE   19   16
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              10               19
  YES              9               16
[1] 2 2
[1] FALSE
                  vv
clus               UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  PIK3CA MUTATED                                                                     5
  PIK3CA WILD-TYPE                                                                  19
                  vv
clus               UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  PIK3CA MUTATED                                                 8
  PIK3CA WILD-TYPE                                              12
                  vv
clus               UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  PIK3CA MUTATED                                              7
  PIK3CA WILD-TYPE                                            6
D10V4, multiclass
                                                                     clus
vv                                                                    PIK3CA MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              5
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  8
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                     7
                                                                     clus
vv                                                                    PIK3CA WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               19
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   12
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       1                         2    17
  PIK3CA WILD-TYPE     2                         7    27
D10V5, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              2                7
  WHITE                                 17               27
[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"

Clustering(11) Variable = MAMLD1 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2               0  1
  MAMLD1 MUTATED    2  2
  MAMLD1 WILD-TYPE 19 33
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               4               52 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               2               33 
$`MAMLD1 MUTATED`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-ND-A4WC TCGA-NA-A4QY 
       81.70         3.68        25.18         3.75 

$`MAMLD1 WILD-TYPE`
TCGA-N5-A4RN TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4R8 
       34.62         9.57        27.25        20.09        19.30       102.41 
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
       52.31         4.67        59.38        18.08         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       29.95        50.17        67.13        14.70        11.87        32.19 
TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B 
       19.63        17.16        51.75        25.35         0.26        27.19 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S 
       26.63        13.74        26.70        25.68        18.81        12.20 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       21.93        67.17        54.97        35.80        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
      140.35        80.78        27.55        17.79         6.67        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 
       10.42        23.47         5.49         9.80        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
        5.49        14.53        31.20        12.43 

  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
            3.68             0.26 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
           81.70           140.35 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
          14.465           21.010 
[1] "3.7 - 81.7 (14.5)"  "0.3 - 140.3 (21.0)"
[1] "hr=" "1"  
D11V2, continuous
D11V3, binary
                  cls
clus                0  1
  MAMLD1 MUTATED    2  2
  MAMLD1 WILD-TYPE 27 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMLD1 MUTATED      2    2
  MAMLD1 WILD-TYPE   27   23
     clus
vv    MAMLD1 MUTATED MAMLD1 WILD-TYPE
  NO               2               27
  YES              2               23
[1] 2 2
[1] FALSE
                  vv
clus               UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  MAMLD1 MUTATED                                                                     1
  MAMLD1 WILD-TYPE                                                                  23
                  vv
clus               UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  MAMLD1 MUTATED                                                 1
  MAMLD1 WILD-TYPE                                              19
                  vv
clus               UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  MAMLD1 MUTATED                                              2
  MAMLD1 WILD-TYPE                                           11
D11V4, multiclass
                                                                     clus
vv                                                                    MAMLD1 MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              1
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  1
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                     2
                                                                     clus
vv                                                                    MAMLD1 WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               23
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   19
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAMLD1 MUTATED       1                         0     3
  MAMLD1 WILD-TYPE     2                         9    41
D11V5, multiclass
                           clus
vv                          MAMLD1 MUTATED MAMLD1 WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                9
  WHITE                                  3               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"
