[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/22533738/transformed.cor.cli.txt"

nPatients in clinical file=57, in cluster file=56, common to both=56
[1] "Reduce the number of clustering variables from 82 to 79."
[1] 79 56
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24                32 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24                32 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               31                25 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               31                25 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               23                33 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               23                33 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21                35 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21                35 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                46 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                46 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               22                34 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               22                34 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10                46 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10                46 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                53 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                53 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23                33 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23                33 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                48 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                48 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               31                25 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               31                25 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27                29 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27                29 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               21                35 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               21                35 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18                38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18                38 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18                38 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18                38 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               30                26 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               30                26 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6                50 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6                50 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                20                 36 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                20                 36 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                17                 39 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                17                 39 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 51 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 51 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 49 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 49 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                22                 34 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                22                 34 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                 45 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                 45 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                 41 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                 41 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                 49 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                 49 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 52 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 52 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                 46 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                 46 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 50 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 50 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                 47 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                 47 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                 38 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                 38 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                 38 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                 38 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 43 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 43 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                24                 32 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                24                 32 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                29                 27 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                29                 27 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                36                 20 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                36                 20 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                 13 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                 13 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                18                 38 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                18                 38 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                 48 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                 48 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18                38 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18                38 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               15                41 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               15                41 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               10                46 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               10                46 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10                46 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10                46 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22                34 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22                34 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               15                41 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               15                41 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               30                26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               30                26 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34                22 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34                22 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                47 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                47 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               18                38 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               18                38 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                51 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                51 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                49 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                49 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13                43 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13                43 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               12                44 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               12                44 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               24                32 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               24                32 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9                47 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9                47 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               35                21 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               35                21 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               40                16 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               40                16 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                24                 32 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                24                 32 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                20                 36 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                20                 36 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                28                 28 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                28                 28 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                 30 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                 30 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                13                 43 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                13                 43 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                 42 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                 42 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                26                 30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                26                 30 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                27                 29 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                27                 29 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                33                 23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                33                 23 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                32                 24 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                32                 24 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                37                 19 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                37                 19 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                34                 22 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                34                 22 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                 39 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                 39 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 38 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 38 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                20                 36 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                20                 36 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                15                 41 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                15                 41 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                 44 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                 44 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                 48 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                 48 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                 51 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                 51 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                17                 39 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                17                 39 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                33                 23 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                33                 23 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               15                41 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               15                41 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18                38 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18                38 
[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 56 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=33,	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"                "42"                  
freq.contrast "42"               "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 56 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 = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED   11 13
  1P GAIN WILD-TYPE 10 21
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24                31 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13                21 
$`1P GAIN MUTATED`
TCGA-N8-A4PM TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ 
       27.25        20.09        19.30        52.31        59.38        18.08 
TCGA-N5-A4RM TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N7-A4Y5 TCGA-N7-A59B 
        4.87        67.13        32.19        17.16         0.26        27.19 
TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 
       13.74        26.70        25.68        67.17        54.97        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-NF-A4X2 TCGA-N7-A4Y8 
       15.81         3.75        17.79        10.42         2.66        12.43 

$`1P GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-ND-A4WC TCGA-N5-A4RD 
       34.62        81.70         3.68         9.57        25.18         4.67 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC 
       22.52        29.95        50.17        14.70        11.87        19.63 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       51.75        25.35        26.63        18.81        12.20        21.93 
TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-NA-A5I1 
       35.80       140.35        80.78        27.55         6.67        88.11 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU 
       23.47         5.49         9.80        14.86         5.49        14.53 
TCGA-NG-A4VW 
       31.20 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.26              3.68 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            67.17            140.35 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            19.58             22.52 
[1] "0.3 - 67.2 (19.6)"  "3.7 - 140.3 (22.5)"
[1] "hr=" "1.1"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   14  9
  1P GAIN WILD-TYPE 15 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     14    9
  1P GAIN WILD-TYPE   15   15
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               14                15
  YES               9                15
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  1P GAIN MUTATED                                                                     8
  1P GAIN WILD-TYPE                                                                  16
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  1P GAIN MUTATED                                                10
  1P GAIN WILD-TYPE                                               9
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  1P GAIN MUTATED                                              6
  1P GAIN WILD-TYPE                                            7
D1V4, multiclass
                                                                     clus
vv                                                                    1P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               8
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  10
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      6
                                                                     clus
vv                                                                    1P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                16
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     9
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        7
[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
  1P GAIN MUTATED       0                         4    20
  1P GAIN WILD-TYPE     3                         5    23
D1V5, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                  20                23
[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 = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   15 16
  1Q GAIN WILD-TYPE  6 18
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               31                24 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16                18 
$`1Q GAIN MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N8-A4PM TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RA 
       34.62        81.70        27.25        20.09        19.30        52.31 
TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VC 
       59.38        18.08         4.87        67.13        32.19        19.63 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO 
       17.16        51.75        27.19        13.74        26.70        25.68 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV 
       21.93        67.17        54.97        19.86        15.81       140.35 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW 
        3.75        17.79        10.42         2.66        14.53        31.20 
TCGA-N7-A4Y8 
       12.43 

$`1Q GAIN WILD-TYPE`
TCGA-N6-A4VD TCGA-N6-A4VE TCGA-ND-A4WC TCGA-N5-A4RD TCGA-N5-A4RO TCGA-N5-A4RS 
        3.68         9.57        25.18         4.67        22.52        29.95 
TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PI 
       50.17        14.70        11.87        25.35         0.26        26.63 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q4 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R1 
       18.81        12.20        35.80        80.78        27.55         6.67 
TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP 
       88.11        23.47         5.49         9.80        14.86         5.49 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             2.66              0.26 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           140.35             88.11 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           21.930            16.835 
[1] "2.7 - 140.3 (21.9)" "0.3 - 88.1 (16.8)" 
[1] "hr=" "1.9"
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   17 13
  1Q GAIN WILD-TYPE 12 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17   13
  1Q GAIN WILD-TYPE   12   11
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               17                12
  YES              13                11
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  1Q GAIN MUTATED                                                                    14
  1Q GAIN WILD-TYPE                                                                  10
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  1Q GAIN MUTATED                                                 9
  1Q GAIN WILD-TYPE                                              10
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  1Q GAIN MUTATED                                              8
  1Q GAIN WILD-TYPE                                            5
D2V4, multiclass
                                                                     clus
vv                                                                    1Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              14
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   9
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      8
                                                                     clus
vv                                                                    1Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                10
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    10
  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
  1Q GAIN MUTATED       0                         5    26
  1Q GAIN WILD-TYPE     3                         4    17
D2V5, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               5                 4
  WHITE                                  26                17
[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 = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    6 17
  2P GAIN WILD-TYPE 15 17
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               23                32 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               17                17 
$`2P GAIN MUTATED`
TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       18.08        29.95        50.17        14.70        11.87        32.19 
TCGA-N6-A4VC TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A56S TCGA-N9-A4Q1 
       19.63         0.26        27.19        13.74        12.20        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4W6 
       54.97        35.80        80.78         3.75        17.79        10.42 
TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
       23.47         9.80         5.49        14.53        12.43 

$`2P GAIN 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM 
       25.18        19.30        52.31         4.67        59.38         4.87 
TCGA-N5-A4RO TCGA-N5-A4RV TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PI 
       22.52        67.13        17.16        51.75        25.35        26.63 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       26.70        25.68        18.81        21.93        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WF TCGA-NF-A4WX 
      140.35        27.55         6.67        88.11         5.49        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VW 
        2.66        31.20 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.26              2.66 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            80.78            140.35 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            17.79             23.85 
[1] "0.3 - 80.8 (17.8)"  "2.7 - 140.3 (23.9)"
[1] "hr=" "1.7"
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   15  6
  2P GAIN WILD-TYPE 14 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15    6
  2P GAIN WILD-TYPE   14   18
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               15                14
  YES               6                18
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  2P GAIN MUTATED                                                                    10
  2P GAIN WILD-TYPE                                                                  14
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  2P GAIN MUTATED                                                 9
  2P GAIN WILD-TYPE                                              10
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  2P GAIN MUTATED                                              4
  2P GAIN WILD-TYPE                                            9
D3V4, multiclass
                                                                     clus
vv                                                                    2P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              10
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   9
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      4
                                                                     clus
vv                                                                    2P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                14
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    10
  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
  2P GAIN MUTATED       1                         4    18
  2P GAIN WILD-TYPE     2                         5    25
D3V5, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                  18                25
[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 = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    7 14
  2Q GAIN WILD-TYPE 14 20
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21                34 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               14                20 
$`2Q GAIN MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59F TCGA-N6-A4VC 
       52.31        18.08        29.95        50.17        11.87        19.63 
TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-N9-A4Q4 
        0.26        27.19        13.74        12.20        54.97        35.80 
TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4WA 
       19.86       140.35        80.78         3.75        17.79        23.47 
TCGA-NF-A4WU TCGA-NG-A4VU TCGA-N7-A4Y8 
        9.80        14.53        12.43 

$`2Q GAIN 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-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO 
       25.18        19.30         4.67        59.38         4.87        22.52 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       67.13        14.70        32.19        17.16        51.75        25.35 
TCGA-N8-A4PI TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 
       26.63        26.70        25.68        18.81        21.93        67.17 
TCGA-N9-A4Q8 TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WF 
       15.81        27.55         6.67        88.11        10.42         5.49 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW 
       14.86         2.66         5.49        31.20 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.26              2.66 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           140.35             88.11 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           19.630            22.225 
[1] "0.3 - 140.3 (19.6)" "2.7 - 88.1 (22.2)" 
[1] "hr=" "1.1"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   14  5
  2Q GAIN WILD-TYPE 15 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14    5
  2Q GAIN WILD-TYPE   15   19
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               14                15
  YES               5                19
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  2Q GAIN MUTATED                                                                     9
  2Q GAIN WILD-TYPE                                                                  15
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  2Q GAIN MUTATED                                                 8
  2Q GAIN WILD-TYPE                                              11
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  2Q GAIN MUTATED                                              4
  2Q GAIN WILD-TYPE                                            9
D4V4, multiclass
                                                                     clus
vv                                                                    2Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               9
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   8
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      4
                                                                     clus
vv                                                                    2Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                15
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    11
  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
  2Q GAIN MUTATED       1                         4    16
  2Q GAIN WILD-TYPE     2                         5    27
D4V5, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                  16                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(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    4  5
  3P GAIN WILD-TYPE 17 29
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                9                46 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                29 
$`3P GAIN MUTATED`
TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QX 
       26.70        18.81        67.17        54.97        15.81        27.55 
TCGA-ND-A4WA TCGA-NF-A4X2 TCGA-NG-A4VW 
       23.47         2.66        31.20 

$`3P GAIN 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ 
       25.18        19.30        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-A4Y0 
       11.87        32.19        19.63        17.16        51.75        25.35 
TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A56S 
        0.26        27.19        26.63        13.74        25.68        12.20 
TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY 
       21.93        35.80        19.86       140.35        80.78         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WU 
       17.79         6.67        88.11        10.42         5.49         9.80 
TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
       14.86         5.49        14.53        12.43 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.66              0.26 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            67.17            140.35 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           26.700            19.745 
[1] "2.7 - 67.2 (26.7)"  "0.3 - 140.3 (19.7)"
[1] "hr=" "1.4"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    4  6
  3P GAIN WILD-TYPE 25 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4    6
  3P GAIN WILD-TYPE   25   18
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                4                25
  YES               6                18
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  3P GAIN MUTATED                                                                     6
  3P GAIN WILD-TYPE                                                                  18
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  3P GAIN MUTATED                                                 3
  3P GAIN WILD-TYPE                                              16
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  3P GAIN MUTATED                                              1
  3P GAIN WILD-TYPE                                           12
D5V4, multiclass
                                                                     clus
vv                                                                    3P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               6
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   3
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      1
                                                                     clus
vv                                                                    3P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                18
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    16
  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
  3P GAIN MUTATED       2                         1     7
  3P GAIN WILD-TYPE     1                         8    36
D5V5, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               1                 8
  WHITE                                   7                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"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    9 12
  3Q GAIN WILD-TYPE 12 22
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               21                34 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                22 
$`3Q GAIN MUTATED`
TCGA-N5-A4RN TCGA-N6-A4VE TCGA-N8-A4PP TCGA-N5-A4RO TCGA-N6-A4VC TCGA-N7-A4Y5 
       34.62         9.57        20.09        22.52        19.63         0.26 
TCGA-N7-A59B TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       27.19        26.70        18.81        21.93        67.17        54.97 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-ND-A4WA TCGA-NF-A4WX 
       15.81       140.35        80.78        27.55        23.47        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VW TCGA-N7-A4Y8 
        2.66        31.20        12.43 

$`3Q GAIN WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RA 
       81.70         3.68        27.25        25.18        19.30        52.31 
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RU 
        4.67        59.38        18.08         4.87        29.95        50.17 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N6-A4VG 
       67.13        14.70        11.87        32.19        17.16        51.75 
TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4Q4 
       25.35        26.63        13.74        25.68        12.20        35.80 
TCGA-N9-A4Q7 TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       19.86         3.75        17.79         6.67        88.11        10.42 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VU 
        5.49         9.80         5.49        14.53 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.26              3.68 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           140.35             88.11 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            22.52             18.69 
[1] "0.3 - 140.3 (22.5)" "3.7 - 88.1 (18.7)" 
[1] "hr=" "1.3"
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   11 10
  3Q GAIN WILD-TYPE 18 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     11   10
  3Q GAIN WILD-TYPE   18   14
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               11                18
  YES              10                14
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  3Q GAIN MUTATED                                                                    11
  3Q GAIN WILD-TYPE                                                                  13
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  3Q GAIN MUTATED                                                 6
  3Q GAIN WILD-TYPE                                              13
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  3Q GAIN MUTATED                                              5
  3Q GAIN WILD-TYPE                                            8
D6V4, multiclass
                                                                     clus
vv                                                                    3Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   6
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      5
                                                                     clus
vv                                                                    3Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    13
  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
  3Q GAIN MUTATED       2                         3    16
  3Q GAIN WILD-TYPE     1                         6    27
D6V5, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                  16                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(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    4  6
  4P GAIN WILD-TYPE 17 28
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10                45 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6                28 
$`4P GAIN MUTATED`
TCGA-N8-A4PP TCGA-N5-A4RO TCGA-N5-A4RV TCGA-N7-A59B TCGA-N9-A4PZ TCGA-N9-A4Q1 
       20.09        22.52        67.13        27.19        21.93        67.17 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-ND-A4W6 TCGA-NF-A4WX 
       15.81       140.35        10.42        14.86 

$`4P GAIN WILD-TYPE`
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-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
       19.30        52.31         4.67        59.38        18.08         4.87 
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-N8-A4PI TCGA-N8-A4PL 
       17.16        51.75        25.35         0.26        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       26.70        25.68        18.81        12.20        54.97        35.80 
TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 
       19.86        80.78        27.55         3.75        17.79         6.67 
TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP 
       88.11        23.47         5.49         9.80         2.66         5.49 
TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
       14.53        31.20        12.43 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            10.42              0.26 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           140.35             88.11 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           22.225            19.630 
[1] "10.4 - 140.3 (22.2)" "0.3 - 88.1 (19.6)"  
[1] "hr=" "1.4"
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    4  5
  4P GAIN WILD-TYPE 25 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    5
  4P GAIN WILD-TYPE   25   19
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                4                25
  YES               5                19
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  4P GAIN MUTATED                                                                     4
  4P GAIN WILD-TYPE                                                                  20
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  4P GAIN MUTATED                                                 2
  4P GAIN WILD-TYPE                                              17
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  4P GAIN MUTATED                                              4
  4P GAIN WILD-TYPE                                            9
D7V4, multiclass
                                                                     clus
vv                                                                    4P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               4
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   2
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      4
                                                                     clus
vv                                                                    4P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                20
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    17
  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
  4P GAIN MUTATED       0                         4     5
  4P GAIN WILD-TYPE     3                         5    38
D7V5, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                   5                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"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    1  2
  4Q GAIN WILD-TYPE 20 32
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                52 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                32 
$`4Q GAIN MUTATED`
TCGA-N5-A4RV TCGA-N9-A4PZ TCGA-N9-A4Q8 
       67.13        21.93        15.81 

$`4Q GAIN 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ 
       25.18        19.30        52.31         4.67        59.38        18.08 
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F 
        4.87        22.52        29.95        50.17        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-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-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV 
       12.20        67.17        54.97        35.80        19.86       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-NG-A4VW TCGA-N7-A4Y8 
        5.49        14.53        31.20        12.43 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            15.81              0.26 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            67.13            140.35 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           21.930            19.975 
[1] "15.8 - 67.1 (21.9)" "0.3 - 140.3 (20.0)"
[1] "hr=" "1"  
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  3
  4Q GAIN WILD-TYPE 29 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    3
  4Q GAIN WILD-TYPE   29   21
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                29
  YES               3                21
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  4Q GAIN MUTATED                                                                     2
  4Q GAIN WILD-TYPE                                                                  22
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  4Q GAIN MUTATED                                                 0
  4Q GAIN WILD-TYPE                                              19
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  4Q GAIN MUTATED                                              1
  4Q GAIN WILD-TYPE                                           12
D8V4, multiclass
                                                                     clus
vv                                                                    4Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               2
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   0
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      1
                                                                     clus
vv                                                                    4Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                22
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    19
  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
  4Q GAIN MUTATED       0                         0     3
  4Q GAIN WILD-TYPE     3                         9    40
D8V5, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 9
  WHITE                                   3                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(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    6 16
  5P GAIN WILD-TYPE 15 18
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               22                33 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               16                18 
$`5P GAIN MUTATED`
TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PP TCGA-N5-A4RA TCGA-N5-A4RU TCGA-N5-A59E 
       81.70         9.57        20.09        52.31        50.17        14.70 
TCGA-N5-A59F TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PN 
       11.87        17.16        51.75        25.35         0.26        26.70 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-NA-A5I1 
       25.68        18.81        21.93        80.78        17.79        88.11 
TCGA-ND-A4W6 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
       10.42         5.49        14.53        31.20 

$`5P GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N6-A4VD TCGA-N8-A4PM TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RD 
       34.62         3.68        27.25        25.18        19.30         4.67 
TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RV 
       59.38        18.08         4.87        22.52        29.95        67.13 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A56S 
       32.19        19.63        27.19        26.63        13.74        12.20 
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-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU 
       27.55         3.75         6.67        23.47         5.49         9.80 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-N7-A4Y8 
       14.86         2.66        12.43 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.26              2.66 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            88.11            140.35 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            21.01             19.86 
[1] "0.3 - 88.1 (21.0)"  "2.7 - 140.3 (19.9)"
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   13 10
  5P GAIN WILD-TYPE 16 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     13   10
  5P GAIN WILD-TYPE   16   14
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               13                16
  YES              10                14
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  5P GAIN MUTATED                                                                    10
  5P GAIN WILD-TYPE                                                                  14
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  5P GAIN MUTATED                                                 8
  5P GAIN WILD-TYPE                                              11
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  5P GAIN MUTATED                                              5
  5P GAIN WILD-TYPE                                            8
D9V4, multiclass
                                                                     clus
vv                                                                    5P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              10
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   8
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      5
                                                                     clus
vv                                                                    5P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                14
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    11
  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
  5P GAIN MUTATED       1                         3    19
  5P GAIN WILD-TYPE     2                         6    24
D9V5, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                  19                24
[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 = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    1  6
  5Q GAIN WILD-TYPE 20 28
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                48 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                28 
$`5Q GAIN MUTATED`
TCGA-N6-A4VE TCGA-N5-A59E TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-NA-A5I1 
        9.57        14.70        17.16        51.75        25.35        88.11 
TCGA-NG-A4VW 
       31.20 

$`5Q GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       34.62        81.70         3.68        27.25        20.09        25.18 
TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
       19.30        52.31         4.67        59.38        18.08         4.87 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 
       22.52        29.95        50.17        67.13        11.87        32.19 
TCGA-N6-A4VC TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN 
       19.63         0.26        27.19        26.63        13.74        26.70 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       25.68        18.81        12.20        21.93        67.17        54.97 
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-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
        3.75        17.79         6.67        10.42        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
        9.80        14.86         2.66         5.49        14.53        12.43 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             9.57              0.26 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            88.11            140.35 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           25.350            19.975 
[1] "9.6 - 88.1 (25.4)"  "0.3 - 140.3 (20.0)"
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  5
  5Q GAIN WILD-TYPE 26 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    5
  5Q GAIN WILD-TYPE   26   19
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                3                26
  YES               5                19
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  5Q GAIN MUTATED                                                                     6
  5Q GAIN WILD-TYPE                                                                  18
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  5Q GAIN MUTATED                                                 2
  5Q GAIN WILD-TYPE                                              17
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  5Q GAIN MUTATED                                              0
  5Q GAIN WILD-TYPE                                           13
D10V4, multiclass
                                                                     clus
vv                                                                    5Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               6
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   2
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      0
                                                                     clus
vv                                                                    5Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                18
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    17
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       13
[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
  5Q GAIN MUTATED       1                         0     7
  5Q GAIN WILD-TYPE     2                         9    36
D10V5, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 9
  WHITE                                   7                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"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   11 19
  6P GAIN WILD-TYPE 10 15
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               30                25 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               19                15 
$`6P GAIN MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ 
       34.62        81.70         9.57        52.31        59.38        18.08 
TCGA-N5-A4RM TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4VC TCGA-N6-A4VF 
        4.87        50.17        67.13        14.70        19.63        17.16 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N9-A4PZ 
       25.35         0.26        13.74        26.70        25.68        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX 
       67.17        54.97        19.86        15.81        80.78        27.55 
TCGA-NA-A4R0 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU 
       17.79        23.47         5.49        14.86         2.66        14.53 

$`6P GAIN WILD-TYPE`
TCGA-N6-A4VD TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RD 
        3.68        27.25        20.09        25.18        19.30         4.67 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VG TCGA-N7-A59B 
       22.52        29.95        11.87        32.19        51.75        27.19 
TCGA-N8-A4PI TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QY 
       26.63        18.81        12.20        35.80       140.35         3.75 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VW 
        6.67        88.11        10.42         9.80         5.49        31.20 
TCGA-N7-A4Y8 
       12.43 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.26              3.68 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            81.70            140.35 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           20.895            20.090 
[1] "0.3 - 81.7 (20.9)"  "3.7 - 140.3 (20.1)"
[1] "hr=" "1"  
D11V2, continuous
D11V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   17 14
  6P GAIN WILD-TYPE 12 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     17   14
  6P GAIN WILD-TYPE   12   10
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               17                12
  YES              14                10
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  6P GAIN MUTATED                                                                    13
  6P GAIN WILD-TYPE                                                                  11
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  6P GAIN MUTATED                                                12
  6P GAIN WILD-TYPE                                               7
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  6P GAIN MUTATED                                              6
  6P GAIN WILD-TYPE                                            7
D11V4, multiclass
                                                                     clus
vv                                                                    6P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  12
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      6
                                                                     clus
vv                                                                    6P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        7
[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
  6P GAIN MUTATED       2                         3    25
  6P GAIN WILD-TYPE     1                         6    18
D11V5, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                  25                18
[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(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    9 18
  6Q GAIN WILD-TYPE 12 16
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27                28 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               18                16 
$`6Q GAIN MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ 
       34.62        81.70         9.57        52.31        59.38        18.08 
TCGA-N5-A4RM TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4VC TCGA-N6-A4VF 
        4.87        50.17        67.13        14.70        19.63        17.16 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PO TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q7 
       25.35         0.26        25.68        21.93        67.17        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-ND-A4WA TCGA-ND-A4WF 
       15.81        80.78        27.55        17.79        23.47         5.49 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU 
       14.86         2.66        14.53 

$`6Q GAIN WILD-TYPE`
TCGA-N6-A4VD TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RD 
        3.68        27.25        20.09        25.18        19.30         4.67 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VG TCGA-N7-A59B 
       22.52        29.95        11.87        32.19        51.75        27.19 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q3 
       26.63        13.74        26.70        18.81        12.20        54.97 
TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       35.80       140.35         3.75         6.67        88.11        10.42 
TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VW TCGA-N7-A4Y8 
        9.80         5.49        31.20        12.43 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.26              3.68 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            81.70            140.35 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           19.860            21.305 
[1] "0.3 - 81.7 (19.9)"  "3.7 - 140.3 (21.3)"
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   15 12
  6Q GAIN WILD-TYPE 14 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15   12
  6Q GAIN WILD-TYPE   14   12
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               15                14
  YES              12                12
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  6Q GAIN MUTATED                                                                    10
  6Q GAIN WILD-TYPE                                                                  14
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  6Q GAIN MUTATED                                                12
  6Q GAIN WILD-TYPE                                               7
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  6Q GAIN MUTATED                                              5
  6Q GAIN WILD-TYPE                                            8
D12V4, multiclass
                                                                     clus
vv                                                                    6Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              10
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  12
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      5
                                                                     clus
vv                                                                    6Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                14
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     7
  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
  6Q GAIN MUTATED       1                         3    22
  6Q GAIN WILD-TYPE     2                         6    21
D12V5, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                  22                21
[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(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    9 12
  7P GAIN WILD-TYPE 12 22
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               21                34 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               12                22 
$`7P GAIN MUTATED`
TCGA-N5-A4RN TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RU TCGA-N6-A4V9 
       34.62        19.30        52.31         4.67        50.17        32.19 
TCGA-N6-A4VG TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV 
       51.75        21.93        67.17        35.80        19.86       140.35 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 
       27.55         3.75        10.42         5.49        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
        5.49        14.53        12.43 

$`7P GAIN WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       81.70         3.68         9.57        27.25        20.09        25.18 
TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RV 
       59.38        18.08         4.87        22.52        29.95        67.13 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       14.70        11.87        19.63        17.16        25.35         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-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-NA-A4R1 
       12.20        54.97        15.81        80.78        17.79         6.67 
TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NG-A4VW 
       88.11        23.47         9.80        31.20 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             2.66              0.26 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           140.35             88.11 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           19.860            21.305 
[1] "2.7 - 140.3 (19.9)" "0.3 - 88.1 (21.3)" 
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   11  8
  7P GAIN WILD-TYPE 18 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     11    8
  7P GAIN WILD-TYPE   18   16
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               11                18
  YES               8                16
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  7P GAIN MUTATED                                                                    11
  7P GAIN WILD-TYPE                                                                  13
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  7P GAIN MUTATED                                                 8
  7P GAIN WILD-TYPE                                              11
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  7P GAIN MUTATED                                              2
  7P GAIN WILD-TYPE                                           11
D13V4, multiclass
                                                                     clus
vv                                                                    7P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   8
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      2
                                                                     clus
vv                                                                    7P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    11
  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
  7P GAIN MUTATED       0                         5    15
  7P GAIN WILD-TYPE     3                         4    28
D13V5, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               5                 4
  WHITE                                  15                28
[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(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    8 10
  7Q GAIN WILD-TYPE 13 24
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18                37 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               10                24 
$`7Q GAIN MUTATED`
TCGA-N5-A4RN TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N6-A4V9 TCGA-N6-A4VF 
       34.62        19.30        52.31         4.67        32.19        17.16 
TCGA-N6-A4VG TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QX 
       51.75        21.93        67.17        35.80        19.86        27.55 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       23.47         5.49        14.86         2.66         5.49        14.53 

$`7Q GAIN WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       81.70         3.68         9.57        27.25        20.09        25.18 
TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU 
       59.38        18.08         4.87        22.52        29.95        50.17 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       67.13        14.70        11.87        19.63        25.35         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-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY 
       12.20        54.97        15.81       140.35        80.78         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-NF-A4WU TCGA-NG-A4VW 
       17.79         6.67        88.11        10.42         9.80        31.20 
TCGA-N7-A4Y8 
       12.43 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             2.66              0.26 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            67.17            140.35 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           20.895            20.090 
[1] "2.7 - 67.2 (20.9)"  "0.3 - 140.3 (20.1)"
[1] "hr=" "1.1"
D14V2, continuous
D14V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    8  8
  7Q GAIN WILD-TYPE 21 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8    8
  7Q GAIN WILD-TYPE   21   16
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                8                21
  YES               8                16
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  7Q GAIN MUTATED                                                                    11
  7Q GAIN WILD-TYPE                                                                  13
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  7Q GAIN MUTATED                                                 6
  7Q GAIN WILD-TYPE                                              13
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  7Q GAIN MUTATED                                              1
  7Q GAIN WILD-TYPE                                           12
D14V4, multiclass
                                                                     clus
vv                                                                    7Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   6
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      1
                                                                     clus
vv                                                                    7Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    13
  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
  7Q GAIN MUTATED       1                         3    13
  7Q GAIN WILD-TYPE     2                         6    30
D14V5, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                  13                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(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    7 11
  8P GAIN WILD-TYPE 14 23
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18                37 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                23 
$`8P GAIN MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PM TCGA-QM-A5NM TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM 
        9.57        27.25        19.30         4.67        59.38         4.87 
TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PQ TCGA-ND-A4W6 
       17.16        25.35        27.19        26.63        18.81        10.42 
TCGA-ND-A4WA TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW TCGA-N7-A4Y8 
       23.47        14.86         2.66         5.49        31.20        12.43 

$`8P GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-N5-A4RA 
       34.62        81.70         3.68        20.09        25.18        52.31 
TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       18.08        22.52        29.95        50.17        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N8-A4PL 
       11.87        32.19        19.63        51.75         0.26        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       26.70        25.68        12.20        21.93        67.17        54.97 
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-A4WF TCGA-NF-A4WU 
        3.75        17.79         6.67        88.11         5.49         9.80 
TCGA-NG-A4VU 
       14.53 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             2.66              0.26 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            59.38            140.35 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           17.985            22.520 
[1] "2.7 - 59.4 (18.0)"  "0.3 - 140.3 (22.5)"
[1] "hr=" "1.5"
D15V2, continuous
D15V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   11  5
  8P GAIN WILD-TYPE 18 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     11    5
  8P GAIN WILD-TYPE   18   19
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               11                18
  YES               5                19
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  8P GAIN MUTATED                                                                     5
  8P GAIN WILD-TYPE                                                                  19
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  8P GAIN MUTATED                                                10
  8P GAIN WILD-TYPE                                               9
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  8P GAIN MUTATED                                              3
  8P GAIN WILD-TYPE                                           10
D15V4, multiclass
                                                                     clus
vv                                                                    8P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               5
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  10
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      3
                                                                     clus
vv                                                                    8P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                19
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     9
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       10
[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
  8P GAIN MUTATED       1                         1    15
  8P GAIN WILD-TYPE     2                         8    28
D15V5, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 8
  WHITE                                  15                28
[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(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   10 19
  8Q GAIN WILD-TYPE 11 15
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               29                26 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               19                15 
$`8Q GAIN MUTATED`
TCGA-N5-A4RN TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RD 
       34.62         9.57        27.25        20.09        19.30         4.67 
TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       59.38         4.87        19.63        17.16        25.35         0.26 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4Q4 TCGA-N9-A4Q8 
       27.19        26.63        25.68        18.81        35.80        15.81 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WX 
        3.75        17.79        88.11        10.42        23.47        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
        2.66         5.49        14.53        31.20        12.43 

$`8Q GAIN WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-ND-A4WC TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RO 
       81.70         3.68        25.18        52.31        18.08        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-A4VG TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       51.75        13.74        26.70        12.20        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R1 
       54.97        19.86       140.35        80.78        27.55         6.67 
TCGA-ND-A4WF TCGA-NF-A4WU 
        5.49         9.80 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.26              3.68 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            88.11            140.35 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.81             25.94 
[1] "0.3 - 88.1 (18.8)"  "3.7 - 140.3 (25.9)"
[1] "hr=" "1.6"
D16V2, continuous
D16V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   20  7
  8Q GAIN WILD-TYPE  9 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     20    7
  8Q GAIN WILD-TYPE    9   17
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               20                 9
  YES               7                17
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  8Q GAIN MUTATED                                                                    11
  8Q GAIN WILD-TYPE                                                                  13
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  8Q GAIN MUTATED                                                14
  8Q GAIN WILD-TYPE                                               5
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  8Q GAIN MUTATED                                              5
  8Q GAIN WILD-TYPE                                            8
D16V4, multiclass
                                                                     clus
vv                                                                    8Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  14
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      5
                                                                     clus
vv                                                                    8Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     5
  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
  8Q GAIN MUTATED       2                         3    24
  8Q GAIN WILD-TYPE     1                         6    19
D16V5, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                  24                19
[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(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    2  4
  9P GAIN WILD-TYPE 19 30
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6                49 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                30 
$`9P GAIN MUTATED`
TCGA-N8-A4PP TCGA-N5-A4RF TCGA-N5-A4RU TCGA-N7-A59B TCGA-N8-A4PL TCGA-N9-A4PZ 
       20.09        59.38        50.17        27.19        13.74        21.93 

$`9P GAIN WILD-TYPE`
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-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
       19.30        52.31         4.67        18.08         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       29.95        67.13        14.70        11.87        32.19        19.63 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PN 
       17.16        51.75        25.35         0.26        26.63        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-A4QY 
       19.86        15.81       140.35        80.78        27.55         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       17.79         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        9.80        14.86         2.66         5.49        14.53        31.20 
TCGA-N7-A4Y8 
       12.43 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            13.74              0.26 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            59.38            140.35 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            24.56             19.63 
[1] "13.7 - 59.4 (24.6)" "0.3 - 140.3 (19.6)"
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  2
  9P GAIN WILD-TYPE 26 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    2
  9P GAIN WILD-TYPE   26   22
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                3                26
  YES               2                22
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  9P GAIN MUTATED                                                                     2
  9P GAIN WILD-TYPE                                                                  22
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  9P GAIN MUTATED                                                 0
  9P GAIN WILD-TYPE                                              19
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  9P GAIN MUTATED                                              4
  9P GAIN WILD-TYPE                                            9
D17V4, multiclass
                                                                     clus
vv                                                                    9P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               2
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   0
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      4
                                                                     clus
vv                                                                    9P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                22
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    19
  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
  9P GAIN MUTATED       0                         0     6
  9P GAIN WILD-TYPE     3                         9    37
D17V5, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 9
  WHITE                                   6                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(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    7 12
  10P GAIN WILD-TYPE 14 22
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                19                 36 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                 22 
$`10P GAIN MUTATED`
TCGA-N8-A4PP TCGA-N5-A4RJ TCGA-N5-A59F TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       20.09        18.08        11.87        51.75        25.35         0.26 
TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q3 TCGA-NA-A4QX 
       27.19        13.74        26.70        18.81        54.97        27.55 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       10.42        23.47        14.86         2.66         5.49        14.53 
TCGA-NG-A4VW 
       31.20 

$`10P GAIN WILD-TYPE`
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-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO 
       19.30        52.31         4.67        59.38         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC 
       29.95        50.17        67.13        14.70        32.19        19.63 
TCGA-N6-A4VF TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       17.16        26.63        25.68        12.20        21.93        67.17 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY 
       35.80        19.86        15.81       140.35        80.78         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WF TCGA-NF-A4WU TCGA-N7-A4Y8 
       17.79         6.67        88.11         5.49         9.80        12.43 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.26               3.68 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             54.97             140.35 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            18.810             22.225 
[1] "0.3 - 55.0 (18.8)"  "3.7 - 140.3 (22.2)"
[1] "hr=" "1.4"
D18V2, continuous
D18V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   12  7
  10P GAIN WILD-TYPE 17 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    7
  10P GAIN WILD-TYPE   17   17
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                12                 17
  YES                7                 17
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  10P GAIN MUTATED                                                                     8
  10P GAIN WILD-TYPE                                                                  16
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  10P GAIN MUTATED                                                 8
  10P GAIN WILD-TYPE                                              11
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  10P GAIN MUTATED                                              4
  10P GAIN WILD-TYPE                                            9
D18V4, multiclass
                                                                     clus
vv                                                                    10P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                8
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    8
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       4
                                                                     clus
vv                                                                    10P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 16
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     11
  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
  10P GAIN MUTATED       2                         2    15
  10P GAIN WILD-TYPE     1                         7    28
D18V5, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                2                  7
  WHITE                                   15                 28
[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(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    8  8
  10Q GAIN WILD-TYPE 13 26
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                16                 39 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                 26 
$`10Q GAIN MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       34.62        67.13        11.87        51.75        25.35         0.26 
TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-NA-A4QW 
       27.19        13.74        26.70        18.81        67.17        80.78 
TCGA-ND-A4WA TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW 
       23.47         2.66        14.53        31.20 

$`10Q GAIN WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       81.70         3.68         9.57        27.25        20.09        25.18 
TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
       19.30        52.31         4.67        59.38        18.08         4.87 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC 
       22.52        29.95        50.17        14.70        32.19        19.63 
TCGA-N6-A4VF TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q3 
       17.16        26.63        25.68        12.20        21.93        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY 
       35.80        19.86        15.81       140.35        27.55         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WU 
       17.79         6.67        88.11        10.42         5.49         9.80 
TCGA-NF-A4WX TCGA-NF-A5CP TCGA-N7-A4Y8 
       14.86         5.49        12.43 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.26               3.68 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             80.78             140.35 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            26.025             19.630 
[1] "0.3 - 80.8 (26.0)"  "3.7 - 140.3 (19.6)"
[1] "hr=" "1.5"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    8  8
  10Q GAIN WILD-TYPE 21 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      8    8
  10Q GAIN WILD-TYPE   21   16
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 8                 21
  YES                8                 16
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  10Q GAIN MUTATED                                                                     7
  10Q GAIN WILD-TYPE                                                                  17
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  10Q GAIN MUTATED                                                 5
  10Q GAIN WILD-TYPE                                              14
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  10Q GAIN MUTATED                                              5
  10Q GAIN WILD-TYPE                                            8
D19V4, multiclass
                                                                     clus
vv                                                                    10Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       5
                                                                     clus
vv                                                                    10Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     14
  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
  10Q GAIN MUTATED       2                         2    13
  10Q GAIN WILD-TYPE     1                         7    30
D19V5, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                2                  7
  WHITE                                   13                 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(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    2  3
  11P GAIN WILD-TYPE 19 31
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 50 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 31 
$`11P GAIN MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PP TCGA-N8-A4PO TCGA-NA-A4QW TCGA-NG-A4VU 
        9.57        20.09        25.68        80.78        14.53 

$`11P GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62        81.70         3.68        27.25        25.18        19.30 
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-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       26.63        13.74        26.70        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-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.55         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-A4VW TCGA-N7-A4Y8 
       31.20        12.43 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              9.57               0.26 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             80.78             140.35 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            20.090             20.895 
[1] "9.6 - 80.8 (20.1)"  "0.3 - 140.3 (20.9)"
[1] "hr=" "1"  
D20V2, continuous
D20V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  2
  11P GAIN WILD-TYPE 26 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    2
  11P GAIN WILD-TYPE   26   22
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 3                 26
  YES                2                 22
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  11P GAIN MUTATED                                                                     3
  11P GAIN WILD-TYPE                                                                  21
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  11P GAIN MUTATED                                                 1
  11P GAIN WILD-TYPE                                              18
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  11P GAIN MUTATED                                              1
  11P GAIN WILD-TYPE                                           12
D20V4, multiclass
                                                                     clus
vv                                                                    11P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    1
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       1
                                                                     clus
vv                                                                    11P GAIN 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
  11P GAIN MUTATED       0                         1     4
  11P GAIN WILD-TYPE     3                         8    39
D20V5, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  8
  WHITE                                    4                 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(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    3  4
  11Q GAIN WILD-TYPE 18 30
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 48 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 30 
$`11Q GAIN MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PP TCGA-N8-A4PN TCGA-N8-A56S TCGA-N9-A4Q7 TCGA-NA-A4QW 
        9.57        20.09        26.70        12.20        19.86        80.78 
TCGA-NG-A4VU 
       14.53 

$`11Q GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62        81.70         3.68        27.25        25.18        19.30 
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-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 
       26.63        13.74        25.68        18.81        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY 
       54.97        35.80        15.81       140.35        27.55         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       17.79         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW TCGA-N7-A4Y8 
        9.80        14.86         2.66         5.49        31.20        12.43 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              9.57               0.26 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             80.78             140.35 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            19.860             22.225 
[1] "9.6 - 80.8 (19.9)"  "0.3 - 140.3 (22.2)"
[1] "hr=" "1"  
D21V2, continuous
D21V3, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  4
  11Q GAIN WILD-TYPE 26 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    4
  11Q GAIN WILD-TYPE   26   20
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 3                 26
  YES                4                 20
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  11Q GAIN MUTATED                                                                     4
  11Q GAIN WILD-TYPE                                                                  20
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  11Q GAIN MUTATED                                                 1
  11Q GAIN WILD-TYPE                                              18
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  11Q GAIN MUTATED                                              2
  11Q GAIN WILD-TYPE                                           11
D21V4, multiclass
                                                                     clus
vv                                                                    11Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                4
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    1
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       2
                                                                     clus
vv                                                                    11Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 20
  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
  11Q GAIN MUTATED       0                         1     6
  11Q GAIN WILD-TYPE     3                         8    37
D21V5, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  8
  WHITE                                    6                 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(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    7 15
  12P GAIN WILD-TYPE 14 19
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                22                 33 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                 19 
$`12P GAIN MUTATED`
TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N5-A4RO 
       81.70         9.57        27.25         4.67         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A59E TCGA-N6-A4VC TCGA-N7-A4Y5 TCGA-N8-A4PL TCGA-N8-A56S 
       29.95        14.70        19.63         0.26        13.74        12.20 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4R0 TCGA-ND-A4W6 
       67.17        54.97        35.80        19.86        17.79        10.42 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-N7-A4Y8 
        5.49         9.80        14.86        12.43 

$`12P GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RA 
       34.62         3.68        20.09        25.18        19.30        52.31 
TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 
       59.38        18.08        50.17        67.13        11.87        32.19 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PN 
       17.16        51.75        25.35        27.19        26.63        26.70 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       25.68        18.81        21.93        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-NF-A4X2 
       27.55         3.75         6.67        88.11        23.47         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        5.49        14.53        31.20 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.26               2.66 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             81.70             140.35 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             14.78              25.35 
[1] "0.3 - 81.7 (14.8)"  "2.7 - 140.3 (25.4)"
[1] "hr=" "1.7"
D22V2, continuous
D22V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   12  8
  12P GAIN WILD-TYPE 17 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     12    8
  12P GAIN WILD-TYPE   17   16
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                12                 17
  YES                8                 16
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  12P GAIN MUTATED                                                                     8
  12P GAIN WILD-TYPE                                                                  16
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  12P GAIN MUTATED                                                10
  12P GAIN WILD-TYPE                                               9
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  12P GAIN MUTATED                                              4
  12P GAIN WILD-TYPE                                            9
D22V4, multiclass
                                                                     clus
vv                                                                    12P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                8
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   10
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       4
                                                                     clus
vv                                                                    12P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 16
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      9
  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
  12P GAIN MUTATED       0                         5    16
  12P GAIN WILD-TYPE     3                         4    27
D22V5, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                5                  4
  WHITE                                   16                 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(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    5  6
  12Q GAIN WILD-TYPE 16 28
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                 44 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 28 
$`12Q GAIN MUTATED`
TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N7-A4Y5 
       81.70         9.57        27.25         4.67         4.87         0.26 
TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NF-A4WX 
       12.20        67.17        35.80        19.86        14.86 

$`12Q GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RA 
       34.62         3.68        20.09        25.18        19.30        52.31 
TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV 
       59.38        18.08        22.52        29.95        50.17        67.13 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG 
       14.70        11.87        32.19        19.63        17.16        51.75 
TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO 
       25.35        27.19        26.63        13.74        26.70        25.68 
TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       18.81        21.93        54.97        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.55         3.75        17.79         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       23.47         5.49         9.80         2.66         5.49        14.53 
TCGA-NG-A4VW TCGA-N7-A4Y8 
       31.20        12.43 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.26               2.66 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             81.70             140.35 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            14.860             22.225 
[1] "0.3 - 81.7 (14.9)"  "2.7 - 140.3 (22.2)"
[1] "hr=" "1"  
D23V2, continuous
D23V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    5  4
  12Q GAIN WILD-TYPE 24 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5    4
  12Q GAIN WILD-TYPE   24   20
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 5                 24
  YES                4                 20
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  12Q GAIN MUTATED                                                                     4
  12Q GAIN WILD-TYPE                                                                  20
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  12Q GAIN MUTATED                                                 5
  12Q GAIN WILD-TYPE                                              14
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  12Q GAIN MUTATED                                              2
  12Q GAIN WILD-TYPE                                           11
D23V4, multiclass
                                                                     clus
vv                                                                    12Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                4
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       2
                                                                     clus
vv                                                                    12Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 20
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     14
  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
  12Q GAIN MUTATED       0                         3     7
  12Q GAIN WILD-TYPE     3                         6    36
D23V5, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                    7                 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"

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    5 10
  13Q GAIN WILD-TYPE 16 24
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                 40 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                 24 
$`13Q GAIN MUTATED`
TCGA-N5-A4RF TCGA-N5-A59E TCGA-N5-A59F TCGA-N7-A4Y5 TCGA-N8-A4PL TCGA-N8-A4PN 
       59.38        14.70        11.87         0.26        13.74        26.70 
TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QY TCGA-ND-A4W6 TCGA-ND-A4WA 
       35.80        15.81        80.78         3.75        10.42        23.47 
TCGA-NF-A4WX TCGA-NG-A4VU TCGA-N7-A4Y8 
       14.86        14.53        12.43 

$`13Q GAIN 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM 
       25.18        19.30        52.31         4.67        18.08         4.87 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VC 
       22.52        29.95        50.17        67.13        32.19        19.63 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PO 
       17.16        51.75        25.35        27.19        26.63        25.68 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 
       18.81        12.20        21.93        67.17        54.97        19.86 
TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WF 
      140.35        27.55        17.79         6.67        88.11         5.49 
TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW 
        9.80         2.66         5.49        31.20 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.26               2.66 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             80.78             140.35 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             14.70              23.85 
[1] "0.3 - 80.8 (14.7)"  "2.7 - 140.3 (23.9)"
[1] "hr=" "1.5"
D24V2, continuous
D24V3, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    9  5
  13Q GAIN WILD-TYPE 20 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      9    5
  13Q GAIN WILD-TYPE   20   19
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 9                 20
  YES                5                 19
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  13Q GAIN MUTATED                                                                     5
  13Q GAIN WILD-TYPE                                                                  19
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  13Q GAIN MUTATED                                                 7
  13Q GAIN WILD-TYPE                                              12
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  13Q GAIN MUTATED                                              3
  13Q GAIN WILD-TYPE                                           10
D24V4, multiclass
                                                                     clus
vv                                                                    13Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                5
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       3
                                                                     clus
vv                                                                    13Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 19
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     12
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        10
[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
  13Q GAIN MUTATED       1                         3    10
  13Q GAIN WILD-TYPE     2                         6    33
D24V5, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                   10                 33
[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(25) Variable = 14Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    1  6
  14Q GAIN WILD-TYPE 20 28
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                 48 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                 28 
$`14Q GAIN MUTATED`
TCGA-N6-A4VE TCGA-N5-A4RF TCGA-N6-A4VF TCGA-N9-A4Q8 TCGA-NA-A4QY TCGA-NF-A5CP 
        9.57        59.38        17.16        15.81         3.75         5.49 
TCGA-N7-A4Y8 
       12.43 

$`14Q GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       34.62        81.70         3.68        27.25        20.09        25.18 
TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
       19.30        52.31         4.67        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-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI 
       19.63        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-NA-A4QV TCGA-NA-A4QW 
       67.17        54.97        35.80        19.86       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
       27.55        17.79         6.67        88.11        10.42        23.47 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW 
        5.49         9.80        14.86         2.66        14.53        31.20 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.75               0.26 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             59.38             140.35 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            12.430             22.995 
[1] "3.8 - 59.4 (12.4)"  "0.3 - 140.3 (23.0)"
[1] "hr=" "2.7"
D25V2, continuous
D25V3, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    4  3
  14Q GAIN WILD-TYPE 25 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    3
  14Q GAIN WILD-TYPE   25   21
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 4                 25
  YES                3                 21
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  14Q GAIN MUTATED                                                                     4
  14Q GAIN WILD-TYPE                                                                  20
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  14Q GAIN MUTATED                                                 2
  14Q GAIN WILD-TYPE                                              17
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  14Q GAIN MUTATED                                              1
  14Q GAIN WILD-TYPE                                           12
D25V4, multiclass
                                                                     clus
vv                                                                    14Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                4
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    2
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       1
                                                                     clus
vv                                                                    14Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 20
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     17
  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
  14Q GAIN MUTATED       0                         0     7
  14Q GAIN WILD-TYPE     3                         9    36
D25V5, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  9
  WHITE                                    7                 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"

Clustering(26) Variable = 15Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    2  2
  15Q GAIN WILD-TYPE 19 32
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 51 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 32 
$`15Q GAIN MUTATED`
TCGA-N5-A4RA TCGA-N5-A59E TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       52.31        14.70        35.80        19.86 

$`15Q GAIN 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-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
       25.18        19.30         4.67        59.38        18.08         4.87 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 
       22.52        29.95        50.17        67.13        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-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       21.93        67.17        54.97        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.55         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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             14.70               0.26 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             52.31             140.35 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             27.83              20.09 
[1] "14.7 - 52.3 (27.8)" "0.3 - 140.3 (20.1)"
[1] "hr=" "1.5"
D26V2, continuous
D26V3, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    2  1
  15Q GAIN WILD-TYPE 27 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    1
  15Q GAIN WILD-TYPE   27   23
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 2                 27
  YES                1                 23
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  15Q GAIN MUTATED                                                                     2
  15Q GAIN WILD-TYPE                                                                  22
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  15Q GAIN MUTATED                                                 2
  15Q GAIN WILD-TYPE                                              17
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  15Q GAIN MUTATED                                              0
  15Q GAIN WILD-TYPE                                           13
D26V4, multiclass
                                                                     clus
vv                                                                    15Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                2
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    2
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       0
                                                                     clus
vv                                                                    15Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 22
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     17
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        13
[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
  15Q GAIN MUTATED       0                         2     2
  15Q GAIN WILD-TYPE     3                         7    41
D26V5, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                2                  7
  WHITE                                    2                 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"

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    4  6
  16P GAIN WILD-TYPE 17 28
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                 45 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 28 
$`16P GAIN MUTATED`
TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N6-A4VG TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A56S 
       18.08         4.87        51.75        26.70        25.68        12.20 
TCGA-N9-A4Q1 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY 
       67.17       140.35        27.55         3.75 

$`16P GAIN 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RO 
       25.18        19.30        52.31         4.67        59.38        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-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       13.74        18.81        21.93        54.97        35.80        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       15.81        80.78        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 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.75               0.26 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            140.35              88.11 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             26.19              19.86 
[1] "3.8 - 140.3 (26.2)" "0.3 - 88.1 (19.9)" 
[1] "hr=" "1.3"
D27V2, continuous
D27V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    6  4
  16P GAIN WILD-TYPE 23 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6    4
  16P GAIN WILD-TYPE   23   20
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 6                 23
  YES                4                 20
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  16P GAIN MUTATED                                                                     4
  16P GAIN WILD-TYPE                                                                  20
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  16P GAIN MUTATED                                                 5
  16P GAIN WILD-TYPE                                              14
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  16P GAIN MUTATED                                              1
  16P GAIN WILD-TYPE                                           12
D27V4, multiclass
                                                                     clus
vv                                                                    16P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                4
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       1
                                                                     clus
vv                                                                    16P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 20
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     14
  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
  16P GAIN MUTATED       0                         3     7
  16P GAIN WILD-TYPE     3                         6    36
D27V5, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                    7                 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"

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    3  3
  16Q GAIN WILD-TYPE 18 31
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 49 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 31 
$`16Q GAIN MUTATED`
TCGA-N5-A4RM TCGA-N6-A4VG TCGA-N8-A4PO TCGA-N8-A56S TCGA-NA-A4QV TCGA-NA-A4QX 
        4.87        51.75        25.68        12.20       140.35        27.55 

$`16Q GAIN 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ 
       25.18        19.30        52.31         4.67        59.38        18.08 
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-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B 
       32.19        19.63        17.16        25.35         0.26        27.19 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 
       26.63        13.74        26.70        18.81        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QY 
       54.97        35.80        19.86        15.81        80.78         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       17.79         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        9.80        14.86         2.66         5.49        14.53        31.20 
TCGA-N7-A4Y8 
       12.43 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              4.87               0.26 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            140.35              88.11 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            26.615             19.860 
[1] "4.9 - 140.3 (26.6)" "0.3 - 88.1 (19.9)" 
[1] "hr=" "1.7"
D28V2, continuous
D28V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4  2
  16Q GAIN WILD-TYPE 25 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    2
  16Q GAIN WILD-TYPE   25   22
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 4                 25
  YES                2                 22
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  16Q GAIN MUTATED                                                                     3
  16Q GAIN WILD-TYPE                                                                  21
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  16Q GAIN MUTATED                                                 3
  16Q GAIN WILD-TYPE                                              16
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  16Q GAIN MUTATED                                              0
  16Q GAIN WILD-TYPE                                           13
D28V4, multiclass
                                                                     clus
vv                                                                    16Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    3
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       0
                                                                     clus
vv                                                                    16Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 21
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     16
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        13
[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
  16Q GAIN MUTATED       0                         2     4
  16Q GAIN WILD-TYPE     3                         7    39
D28V5, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                2                  7
  WHITE                                    4                 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(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    5  4
  17P GAIN WILD-TYPE 16 30
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                 46 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 30 
$`17P GAIN MUTATED`
TCGA-N5-A4RV TCGA-N6-A4VF TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N9-A4Q1 
       67.13        17.16        27.19        13.74        26.70        67.17 
TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-ND-A4W6 
       19.86        80.78        10.42 

$`17P GAIN 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ 
       25.18        19.30        52.31         4.67        59.38        18.08 
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F 
        4.87        22.52        29.95        50.17        14.70        11.87 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PI 
       32.19        19.63        51.75        25.35         0.26        26.63 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       25.68        18.81        12.20        21.93        54.97        35.80 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 
       15.81       140.35        27.55         3.75        17.79         6.67 
TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 
       88.11        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 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             10.42               0.26 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             80.78             140.35 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             26.70              19.86 
[1] "10.4 - 80.8 (26.7)" "0.3 - 140.3 (19.9)"
[1] "hr=" "1.9"
D29V2, continuous
D29V3, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    3  5
  17P GAIN WILD-TYPE 26 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    5
  17P GAIN WILD-TYPE   26   19
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 3                 26
  YES                5                 19
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  17P GAIN MUTATED                                                                     5
  17P GAIN WILD-TYPE                                                                  19
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  17P GAIN MUTATED                                                 1
  17P GAIN WILD-TYPE                                              18
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  17P GAIN MUTATED                                              3
  17P GAIN WILD-TYPE                                           10
D29V4, multiclass
                                                                     clus
vv                                                                    17P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                5
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    1
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       3
                                                                     clus
vv                                                                    17P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 19
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     18
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        10
[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
  17P GAIN MUTATED       0                         3     6
  17P GAIN WILD-TYPE     3                         6    37
D29V5, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                    6                 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(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    7 11
  17Q GAIN WILD-TYPE 14 23
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                 37 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                11                 23 
$`17Q GAIN MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N5-A4RJ TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4VF 
        9.57        27.25        18.08        50.17        67.13        17.16 
TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N9-A4PZ TCGA-N9-A4Q1 
        0.26        27.19        13.74        26.70        21.93        67.17 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-NA-A4QY TCGA-ND-A4W6 TCGA-ND-A4WA 
       35.80        19.86        80.78         3.75        10.42        23.47 

$`17Q GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62        81.70         3.68        20.09        25.18        19.30 
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS 
       52.31         4.67        59.38         4.87        22.52        29.95 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y0 
       14.70        11.87        32.19        19.63        51.75        25.35 
TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-N9-A4Q8 
       26.63        25.68        18.81        12.20        54.97        15.81 
TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WF 
      140.35        27.55        17.79         6.67        88.11         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        9.80        14.86         2.66         5.49        14.53        31.20 
TCGA-N7-A4Y8 
       12.43 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.26               2.66 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             80.78             140.35 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             22.70              19.63 
[1] "0.3 - 80.8 (22.7)"  "2.7 - 140.3 (19.6)"
[1] "hr=" "1"  
D30V2, continuous
D30V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    9  7
  17Q GAIN WILD-TYPE 20 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      9    7
  17Q GAIN WILD-TYPE   20   17
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 9                 20
  YES                7                 17
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  17Q GAIN MUTATED                                                                     8
  17Q GAIN WILD-TYPE                                                                  16
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  17Q GAIN MUTATED                                                 5
  17Q GAIN WILD-TYPE                                              14
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  17Q GAIN MUTATED                                              5
  17Q GAIN WILD-TYPE                                            8
D30V4, multiclass
                                                                     clus
vv                                                                    17Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                8
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       5
                                                                     clus
vv                                                                    17Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 16
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     14
  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
  17Q GAIN MUTATED       1                         4    13
  17Q GAIN WILD-TYPE     2                         5    30
D30V5, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                4                  5
  WHITE                                   13                 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(31) Variable = 18P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    8 10
  18P GAIN WILD-TYPE 13 24
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                 37 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                 24 
$`18P GAIN MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N5-A4RU TCGA-N5-A4RV 
       34.62        81.70         9.57        27.25        50.17        67.13 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG 
       14.70        11.87        32.19        19.63        17.16        51.75 
TCGA-N7-A59B TCGA-N8-A4PO TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-NA-A4R0 TCGA-ND-A4WF 
       27.19        25.68        21.93        67.17        17.79         5.49 

$`18P GAIN WILD-TYPE`
TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD 
        3.68        20.09        25.18        19.30        52.31         4.67 
TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N7-A4Y0 
       59.38        18.08         4.87        22.52        29.95        25.35 
TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S 
        0.26        26.63        13.74        26.70        18.81        12.20 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       54.97        35.80        19.86        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
       27.55         3.75         6.67        88.11        10.42        23.47 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        9.80        14.86         2.66         5.49        14.53        31.20 
TCGA-N7-A4Y8 
       12.43 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              5.49               0.26 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             81.70             140.35 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            26.435             19.300 
[1] "5.5 - 81.7 (26.4)"  "0.3 - 140.3 (19.3)"
[1] "hr=" "1.4"
D31V2, continuous
D31V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8  9
  18P GAIN WILD-TYPE 21 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    9
  18P GAIN WILD-TYPE   21   15
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 8                 21
  YES                9                 15
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  18P GAIN MUTATED                                                                     7
  18P GAIN WILD-TYPE                                                                  17
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  18P GAIN MUTATED                                                 4
  18P GAIN WILD-TYPE                                              15
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  18P GAIN MUTATED                                              7
  18P GAIN WILD-TYPE                                            6
D31V4, multiclass
                                                                     clus
vv                                                                    18P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    4
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       7
                                                                     clus
vv                                                                    18P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     15
  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
  18P GAIN MUTATED       0                         3    15
  18P GAIN WILD-TYPE     3                         6    28
D31V5, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                   15                 28
[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(32) Variable = 18Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    4  9
  18Q GAIN WILD-TYPE 17 25
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 42 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                 25 
$`18Q GAIN MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RU TCGA-N5-A59E 
        9.57        27.25        59.38         4.87        50.17        14.70 
TCGA-N5-A59F TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A59B TCGA-N9-A4PZ TCGA-NA-A4R0 
       11.87        17.16        51.75        27.19        21.93        17.79 
TCGA-ND-A4WF 
        5.49 

$`18Q GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62        81.70         3.68        20.09        25.18        19.30 
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RV 
       52.31         4.67        18.08        22.52        29.95        67.13 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PL 
       32.19        19.63        25.35         0.26        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       26.70        25.68        18.81        12.20        67.17        54.97 
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-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU 
        3.75         6.67        88.11        10.42        23.47         9.80 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
       14.86         2.66         5.49        14.53        31.20        12.43 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              4.87               0.26 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             59.38             140.35 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            17.790             21.305 
[1] "4.9 - 59.4 (17.8)"  "0.3 - 140.3 (21.3)"
[1] "hr=" "1.4"
D32V2, continuous
D32V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    6  6
  18Q GAIN WILD-TYPE 23 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6    6
  18Q GAIN WILD-TYPE   23   18
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 6                 23
  YES                6                 18
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  18Q GAIN MUTATED                                                                     4
  18Q GAIN WILD-TYPE                                                                  20
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  18Q GAIN MUTATED                                                 4
  18Q GAIN WILD-TYPE                                              15
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  18Q GAIN MUTATED                                              5
  18Q GAIN WILD-TYPE                                            8
D32V4, multiclass
                                                                     clus
vv                                                                    18Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                4
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    4
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       5
                                                                     clus
vv                                                                    18Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 20
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     15
  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
  18Q GAIN MUTATED       0                         1    12
  18Q GAIN WILD-TYPE     3                         8    31
D32V5, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  8
  WHITE                                   12                 31
[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(33) Variable = 19P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   12 11
  19P GAIN WILD-TYPE  9 23
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                23                 32 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                 23 
$`19P GAIN MUTATED`
TCGA-N5-A4RN TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RV 
       34.62         9.57        27.25        20.09        19.30        67.13 
TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PO TCGA-N8-A4PQ 
       19.63        51.75         0.26        27.19        25.68        18.81 
TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 
       35.80        15.81        80.78        27.55         3.75        17.79 
TCGA-ND-A4W6 TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       10.42        14.86         2.66         5.49        14.53 

$`19P GAIN WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-ND-A4WC TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF 
       81.70         3.68        25.18        52.31         4.67        59.38 
TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E 
       18.08         4.87        22.52        29.95        50.17        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PL 
       11.87        32.19        17.16        25.35        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 
       26.70        12.20        21.93        67.17        54.97        19.86 
TCGA-NA-A4QV TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU 
      140.35         6.67        88.11        23.47         5.49         9.80 
TCGA-NG-A4VW TCGA-N7-A4Y8 
       31.20        12.43 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.26               3.68 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             80.78             140.35 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            19.300             22.995 
[1] "0.3 - 80.8 (19.3)"  "3.7 - 140.3 (23.0)"
[1] "hr=" "1.2"
D33V2, continuous
D33V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   15  7
  19P GAIN WILD-TYPE 14 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     15    7
  19P GAIN WILD-TYPE   14   17
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                15                 14
  YES                7                 17
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  19P GAIN MUTATED                                                                    11
  19P GAIN WILD-TYPE                                                                  13
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  19P GAIN MUTATED                                                 8
  19P GAIN WILD-TYPE                                              11
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  19P GAIN MUTATED                                              5
  19P GAIN WILD-TYPE                                            8
D33V4, multiclass
                                                                     clus
vv                                                                    19P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    8
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       5
                                                                     clus
vv                                                                    19P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     11
  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
  19P GAIN MUTATED       1                         3    19
  19P GAIN WILD-TYPE     2                         6    24
D33V5, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                   19                 24
[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(34) Variable = 19Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   11 17
  19Q GAIN WILD-TYPE 10 17
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                28                 27 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                 17 
$`19Q GAIN MUTATED`
TCGA-N5-A4RN TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RJ 
       34.62         9.57        27.25        20.09        19.30        18.08 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N8-A4PL 
       67.13        14.70        19.63        51.75         0.26        13.74 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX 
       25.68        18.81        35.80        15.81        80.78        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WX 
        3.75        17.79        88.11        10.42        23.47        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
        2.66         5.49        14.53        12.43 

$`19Q GAIN WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-ND-A4WC TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF 
       81.70         3.68        25.18        52.31         4.67        59.38 
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59F TCGA-N6-A4V9 
        4.87        22.52        29.95        50.17        11.87        32.19 
TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PN TCGA-N8-A56S 
       17.16        25.35        27.19        26.63        26.70        12.20 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4R1 
       21.93        67.17        54.97        19.86       140.35         6.67 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NG-A4VW 
        5.49         9.80        31.20 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.26               3.68 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             88.11             140.35 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            18.445             25.350 
[1] "0.3 - 88.1 (18.4)"  "3.7 - 140.3 (25.4)"
[1] "hr=" "1.2"
D34V2, continuous
D34V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   20  8
  19Q GAIN WILD-TYPE  9 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     20    8
  19Q GAIN WILD-TYPE    9   16
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                20                  9
  YES                8                 16
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  19Q GAIN MUTATED                                                                    13
  19Q GAIN WILD-TYPE                                                                  11
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  19Q GAIN MUTATED                                                12
  19Q GAIN WILD-TYPE                                               7
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  19Q GAIN MUTATED                                              4
  19Q GAIN WILD-TYPE                                            9
D34V4, multiclass
                                                                     clus
vv                                                                    19Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   12
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       4
                                                                     clus
vv                                                                    19Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      7
  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
  19Q GAIN MUTATED       2                         3    23
  19Q GAIN WILD-TYPE     1                         6    20
D34V5, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                   23                 20
[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(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   12 24
  20P GAIN WILD-TYPE  9 10
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                36                 19 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                 10 
$`20P GAIN MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-QM-A5NM TCGA-N5-A4RA 
       34.62        81.70         9.57        27.25        19.30        52.31 
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV 
        4.67        59.38         4.87        29.95        50.17        67.13 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N8-A4PL 
       14.70        11.87        32.19        17.16        25.35        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       26.70        25.68        21.93        67.17        35.80        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       15.81        27.55         3.75         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
       23.47         5.49        14.86         5.49        14.53        12.43 

$`20P GAIN WILD-TYPE`
TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N6-A4VC 
        3.68        20.09        25.18        18.08        22.52        19.63 
TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PQ TCGA-N8-A56S 
       51.75         0.26        27.19        26.63        18.81        12.20 
TCGA-N9-A4Q3 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-NF-A4WU TCGA-NF-A4X2 
       54.97       140.35        80.78        17.79         9.80         2.66 
TCGA-NG-A4VW 
       31.20 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              3.75               0.26 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             88.11             140.35 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            20.895             20.090 
[1] "3.8 - 88.1 (20.9)"  "0.3 - 140.3 (20.1)"
[1] "hr=" "1.3"
D35V2, continuous
D35V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   16 18
  20P GAIN WILD-TYPE 13  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     16   18
  20P GAIN WILD-TYPE   13    6
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                16                 13
  YES               18                  6
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  20P GAIN MUTATED                                                                    15
  20P GAIN WILD-TYPE                                                                   9
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  20P GAIN MUTATED                                                12
  20P GAIN WILD-TYPE                                               7
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  20P GAIN MUTATED                                              9
  20P GAIN WILD-TYPE                                            4
D35V4, multiclass
                                                                     clus
vv                                                                    20P GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               15
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   12
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       9
                                                                     clus
vv                                                                    20P GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                  9
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                         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"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       1                         7    27
  20P GAIN WILD-TYPE     2                         2    16
D35V5, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                7                  2
  WHITE                                   27                 16
[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(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   16 27
  20Q GAIN WILD-TYPE  5  7
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                 12 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                27                  7 
$`20Q GAIN MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-QM-A5NM TCGA-N5-A4RA 
       34.62        81.70         9.57        27.25        19.30        52.31 
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RU 
        4.67        59.38        18.08         4.87        29.95        50.17 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N6-A4VG 
       67.13        14.70        11.87        32.19        17.16        51.75 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO 
       25.35         0.26        26.63        13.74        26.70        25.68 
TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       18.81        21.93        54.97        35.80        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
      140.35        27.55         3.75        17.79         6.67        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU 
       10.42        23.47         5.49        14.86         5.49        14.53 
TCGA-N7-A4Y8 
       12.43 

$`20Q GAIN WILD-TYPE`
TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-N5-A4RO TCGA-N6-A4VC TCGA-N7-A59B 
        3.68        20.09        25.18        22.52        19.63        27.19 
TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-NA-A4QW TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NG-A4VW 
       12.20        67.17        80.78         9.80         2.66        31.20 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.26               2.66 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            140.35              80.78 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            19.860             21.305 
[1] "0.3 - 140.3 (19.9)" "2.7 - 80.8 (21.3)" 
[1] "hr=" "1"  
D36V2, continuous
D36V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   22 19
  20Q GAIN WILD-TYPE  7  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     22   19
  20Q GAIN WILD-TYPE    7    5
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                22                  7
  YES               19                  5
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  20Q GAIN MUTATED                                                                    17
  20Q GAIN WILD-TYPE                                                                   7
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  20Q GAIN MUTATED                                                17
  20Q GAIN WILD-TYPE                                               2
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  20Q GAIN MUTATED                                              9
  20Q GAIN WILD-TYPE                                            4
D36V4, multiclass
                                                                     clus
vv                                                                    20Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   17
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       9
                                                                     clus
vv                                                                    20Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                  7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      2
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                         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"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       1                         7    34
  20Q GAIN WILD-TYPE     2                         2     9
D36V5, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                7                  2
  WHITE                                   34                  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"

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    7 10
  21Q GAIN WILD-TYPE 14 24
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                17                 38 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 24 
$`21Q GAIN MUTATED`
TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RV TCGA-N5-A59F 
       81.70         9.57        18.08         4.87        67.13        11.87 
TCGA-N6-A4VG TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 
       51.75        26.70        25.68        18.81        21.93        67.17 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-ND-A4WF 
       15.81       140.35        17.79        10.42         5.49 

$`21Q GAIN WILD-TYPE`
TCGA-N5-A4RN TCGA-N6-A4VD TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62         3.68        27.25        20.09        25.18        19.30 
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU 
       52.31         4.67        59.38        22.52        29.95        50.17 
TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       14.70        32.19        19.63        17.16        25.35         0.26 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       27.19        26.63        13.74        12.20        54.97        35.80 
TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 
       19.86        80.78        27.55         3.75         6.67        88.11 
TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       23.47         9.80        14.86         2.66         5.49        14.53 
TCGA-NG-A4VW TCGA-N7-A4Y8 
       31.20        12.43 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              4.87               0.26 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            140.35              88.11 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            18.810             21.305 
[1] "4.9 - 140.3 (18.8)" "0.3 - 88.1 (21.3)" 
[1] "hr=" "1.2"
D37V2, continuous
D37V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    8 10
  21Q GAIN WILD-TYPE 21 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8   10
  21Q GAIN WILD-TYPE   21   14
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 8                 21
  YES               10                 14
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  21Q GAIN MUTATED                                                                     7
  21Q GAIN WILD-TYPE                                                                  17
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  21Q GAIN MUTATED                                                 7
  21Q GAIN WILD-TYPE                                              12
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  21Q GAIN MUTATED                                              4
  21Q GAIN WILD-TYPE                                            9
D37V4, multiclass
                                                                     clus
vv                                                                    21Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       4
                                                                     clus
vv                                                                    21Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     12
  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
  21Q GAIN MUTATED       1                         5    12
  21Q GAIN WILD-TYPE     2                         4    31
D37V5, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                5                  4
  WHITE                                   12                 31
[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(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    5  2
  22Q GAIN WILD-TYPE 16 32
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 48 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 32 
$`22Q GAIN MUTATED`
TCGA-N5-A4RF TCGA-N5-A4RU TCGA-N5-A59E TCGA-N6-A4VG TCGA-N7-A59B TCGA-NA-A4QW 
       59.38        50.17        14.70        51.75        27.19        80.78 
TCGA-NF-A4WX 
       14.86 

$`22Q GAIN 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM 
       25.18        19.30        52.31         4.67        18.08         4.87 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       22.52        29.95        67.13        11.87        32.19        19.63 
TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN 
       17.16        25.35         0.26        26.63        13.74        26.70 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       25.68        18.81        12.20        21.93        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY 
       35.80        19.86        15.81       140.35        27.55         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       17.79         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
        9.80         2.66         5.49        14.53        31.20        12.43 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             14.70               0.26 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             80.78             140.35 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            50.170             19.745 
[1] "14.7 - 80.8 (50.2)" "0.3 - 140.3 (19.7)"
[1] "hr=" "3.5"
D38V2, continuous
D38V3, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  3
  22Q GAIN WILD-TYPE 25 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    3
  22Q GAIN WILD-TYPE   25   21
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 4                 25
  YES                3                 21
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  22Q GAIN MUTATED                                                                     3
  22Q GAIN WILD-TYPE                                                                  21
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  22Q GAIN MUTATED                                                 2
  22Q GAIN WILD-TYPE                                              17
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  22Q GAIN MUTATED                                              3
  22Q GAIN WILD-TYPE                                           10
D38V4, multiclass
                                                                     clus
vv                                                                    22Q GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    2
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       3
                                                                     clus
vv                                                                    22Q GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 21
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     17
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        10
[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
  22Q GAIN MUTATED       1                         0     6
  22Q GAIN WILD-TYPE     2                         9    37
D38V5, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  9
  WHITE                                    6                 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(39) Variable = XP GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED    6 11
  XP GAIN WILD-TYPE 15 23
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               17                38 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               11                23 
$`XP GAIN MUTATED`
TCGA-N5-A4RT TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO 
       81.70        52.31         4.67        59.38         4.87        22.52 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N9-A4Q1 TCGA-N9-A4Q8 
       14.70        11.87        25.35        27.19        67.17        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW 
      140.35        80.78         2.66        14.53        31.20 

$`XP GAIN 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-A4RJ TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4V9 
       19.30        18.08        29.95        50.17        67.13        32.19 
TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PL 
       19.63        17.16        51.75         0.26        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q3 
       26.70        25.68        18.81        12.20        21.93        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 
       35.80        19.86        27.55         3.75        17.79         6.67 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX 
       88.11        10.42        23.47         5.49         9.80        14.86 
TCGA-NF-A5CP TCGA-N7-A4Y8 
        5.49        12.43 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             2.66              0.26 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           140.35             88.11 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           25.350            19.745 
[1] "2.7 - 140.3 (25.4)" "0.3 - 88.1 (19.7)" 
[1] "hr=" "1.2"
D39V2, continuous
D39V3, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    7  9
  XP GAIN WILD-TYPE 22 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    9
  XP GAIN WILD-TYPE   22   15
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                7                22
  YES               9                15
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  XP GAIN MUTATED                                                                     7
  XP GAIN WILD-TYPE                                                                  17
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  XP GAIN MUTATED                                                 6
  XP GAIN WILD-TYPE                                              13
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  XP GAIN MUTATED                                              5
  XP GAIN WILD-TYPE                                            8
D39V4, multiclass
                                                                     clus
vv                                                                    XP GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   6
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      5
                                                                     clus
vv                                                                    XP GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    13
  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
  XP GAIN MUTATED       1                         4    13
  XP GAIN WILD-TYPE     2                         5    30
D39V5, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                  13                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(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    5  9
  XQ GAIN WILD-TYPE 16 25
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               14                41 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                25 
$`XQ GAIN MUTATED`
TCGA-N5-A4RT TCGA-N5-A4RD TCGA-N5-A4RU TCGA-N5-A59F TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       81.70         4.67        50.17        11.87        25.35         0.26 
TCGA-N7-A59B TCGA-N8-A4PO TCGA-N9-A4Q1 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-ND-A4WA 
       27.19        25.68        67.17       140.35        80.78        23.47 
TCGA-NG-A4VU TCGA-NG-A4VW 
       14.53        31.20 

$`XQ GAIN 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-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
       19.30        52.31        59.38        18.08         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF 
       29.95        67.13        14.70        32.19        19.63        17.16 
TCGA-N6-A4VG TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S 
       51.75        26.63        13.74        26.70        18.81        12.20 
TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QX 
       21.93        54.97        35.80        19.86        15.81        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WF 
        3.75        17.79         6.67        88.11        10.42         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-N7-A4Y8 
        9.80        14.86         2.66         5.49        12.43 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.26              2.66 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           140.35             88.11 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           26.435            19.300 
[1] "0.3 - 140.3 (26.4)" "2.7 - 88.1 (19.3)" 
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    7  6
  XQ GAIN WILD-TYPE 22 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7    6
  XQ GAIN WILD-TYPE   22   18
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                7                22
  YES               6                18
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  XQ GAIN MUTATED                                                                     6
  XQ GAIN WILD-TYPE                                                                  18
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  XQ GAIN MUTATED                                                 5
  XQ GAIN WILD-TYPE                                              14
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  XQ GAIN MUTATED                                              4
  XQ GAIN WILD-TYPE                                            9
D40V4, multiclass
                                                                     clus
vv                                                                    XQ GAIN MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               6
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      4
                                                                     clus
vv                                                                    XQ GAIN WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                18
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    14
  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
  XQ GAIN MUTATED       2                         4     9
  XQ GAIN WILD-TYPE     1                         5    34
D40V5, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                   9                34
[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(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    2  7
  1P LOSS WILD-TYPE 19 27
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9                46 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                27 
$`1P LOSS MUTATED`
TCGA-N6-A4VE TCGA-N5-A4RD TCGA-N5-A59E TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
        9.57         4.67        14.70        18.81        12.20        21.93 
TCGA-N9-A4Q4 TCGA-NA-A5I1 TCGA-NF-A5CP 
       35.80        88.11         5.49 

$`1P LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       34.62        81.70         3.68        27.25        20.09        25.18 
TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
       19.30        52.31        59.38        18.08         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       29.95        50.17        67.13        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-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 
       13.74        26.70        25.68        67.17        54.97        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-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX 
        6.67        10.42        23.47         5.49         9.80        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
        2.66        14.53        31.20        12.43 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             4.67              0.26 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            88.11            140.35 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           14.700            22.995 
[1] "4.7 - 88.1 (14.7)"  "0.3 - 140.3 (23.0)"
[1] "hr=" "1.6"
D41V2, continuous
D41V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    5  3
  1P LOSS WILD-TYPE 24 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5    3
  1P LOSS WILD-TYPE   24   21
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                5                24
  YES               3                21
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  1P LOSS MUTATED                                                                     6
  1P LOSS WILD-TYPE                                                                  18
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  1P LOSS MUTATED                                                 4
  1P LOSS WILD-TYPE                                              15
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  1P LOSS MUTATED                                              0
  1P LOSS WILD-TYPE                                           13
D41V4, multiclass
                                                                     clus
vv                                                                    1P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               6
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   4
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      0
                                                                     clus
vv                                                                    1P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                18
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    15
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       13
[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
  1P LOSS MUTATED       1                         1     8
  1P LOSS WILD-TYPE     2                         8    35
D41V5, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 8
  WHITE                                   8                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(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    2  7
  1Q LOSS WILD-TYPE 19 27
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9                46 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7                27 
$`1Q LOSS MUTATED`
TCGA-N6-A4VE TCGA-N5-A4RD TCGA-N5-A59E TCGA-N7-A4Y5 TCGA-N8-A4PQ TCGA-N8-A56S 
        9.57         4.67        14.70         0.26        18.81        12.20 
TCGA-N9-A4Q4 TCGA-NA-A5I1 TCGA-NF-A5CP 
       35.80        88.11         5.49 

$`1Q LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       34.62        81.70         3.68        27.25        20.09        25.18 
TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
       19.30        52.31        59.38        18.08         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       29.95        50.17        67.13        11.87        32.19        19.63 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       17.16        51.75        25.35        27.19        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 
       26.70        25.68        21.93        67.17        54.97        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-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX 
        6.67        10.42        23.47         5.49         9.80        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
        2.66        14.53        31.20        12.43 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.26              2.66 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            88.11            140.35 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           12.200            22.995 
[1] "0.3 - 88.1 (12.2)"  "2.7 - 140.3 (23.0)"
[1] "hr=" "1.9"
D42V2, continuous
D42V3, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    6  2
  1Q LOSS WILD-TYPE 23 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6    2
  1Q LOSS WILD-TYPE   23   22
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                6                23
  YES               2                22
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  1Q LOSS MUTATED                                                                     5
  1Q LOSS WILD-TYPE                                                                  19
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  1Q LOSS MUTATED                                                 5
  1Q LOSS WILD-TYPE                                              14
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  1Q LOSS MUTATED                                              0
  1Q LOSS WILD-TYPE                                           13
D42V4, multiclass
                                                                     clus
vv                                                                    1Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               5
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      0
                                                                     clus
vv                                                                    1Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                19
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    14
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       13
[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
  1Q LOSS MUTATED       1                         1     8
  1Q LOSS WILD-TYPE     2                         8    35
D42V5, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 8
  WHITE                                   8                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(43) Variable = 3P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    9 13
  3P LOSS WILD-TYPE 12 21
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22                33 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               13                21 
$`3P LOSS MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF 
        9.57        20.09        19.30        52.31         4.67        59.38 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI 
       11.87        32.19        19.63         0.26        27.19        26.63 
TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QY 
       13.74        25.68        12.20        35.80        19.86         3.75 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU 
        9.80        14.86         5.49        14.53 

$`3P LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-ND-A4WC TCGA-N5-A4RJ 
       34.62        81.70         3.68        27.25        25.18        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-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4PZ 
       17.16        51.75        25.35        26.70        18.81        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       67.17        54.97        15.81       140.35        80.78        27.55 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       17.79         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4X2 TCGA-NG-A4VW TCGA-N7-A4Y8 
        2.66        31.20        12.43 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.26              2.66 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            59.38            140.35 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            17.08             25.18 
[1] "0.3 - 59.4 (17.1)"  "2.7 - 140.3 (25.2)"
[1] "hr=" "1.4"
D43V2, continuous
D43V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   13  6
  3P LOSS WILD-TYPE 16 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     13    6
  3P LOSS WILD-TYPE   16   18
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               13                16
  YES               6                18
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  3P LOSS MUTATED                                                                    10
  3P LOSS WILD-TYPE                                                                  14
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  3P LOSS MUTATED                                                 8
  3P LOSS WILD-TYPE                                              11
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  3P LOSS MUTATED                                              4
  3P LOSS WILD-TYPE                                            9
D43V4, multiclass
                                                                     clus
vv                                                                    3P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              10
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   8
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      4
                                                                     clus
vv                                                                    3P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                14
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    11
  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
  3P LOSS MUTATED       0                         4    17
  3P LOSS WILD-TYPE     3                         5    26
D43V5, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                  17                26
[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(44) Variable = 3Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    6  9
  3Q LOSS WILD-TYPE 15 25
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               15                40 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                25 
$`3Q LOSS MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N8-A4PI 
       52.31         4.67        59.38        11.87        32.19        26.63 
TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QY 
       13.74        25.68        12.20        35.80        19.86         3.75 
TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VU 
        9.80         5.49        14.53 

$`3Q LOSS 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-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS 
       25.18        19.30        18.08         4.87        22.52        29.95 
TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG 
       50.17        67.13        14.70        19.63        17.16        51.75 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4PZ 
       25.35         0.26        27.19        26.70        18.81        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       67.17        54.97        15.81       140.35        80.78        27.55 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       17.79         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VW TCGA-N7-A4Y8 
       14.86         2.66        31.20        12.43 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             3.75              0.26 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            59.38            140.35 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           14.530            22.225 
[1] "3.8 - 59.4 (14.5)"  "0.3 - 140.3 (22.2)"
[1] "hr=" "1.3"
D44V2, continuous
D44V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    9  4
  3Q LOSS WILD-TYPE 20 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      9    4
  3Q LOSS WILD-TYPE   20   20
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                9                20
  YES               4                20
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  3Q LOSS MUTATED                                                                     7
  3Q LOSS WILD-TYPE                                                                  17
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  3Q LOSS MUTATED                                                 6
  3Q LOSS WILD-TYPE                                              13
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  3Q LOSS MUTATED                                              2
  3Q LOSS WILD-TYPE                                           11
D44V4, multiclass
                                                                     clus
vv                                                                    3Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   6
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      2
                                                                     clus
vv                                                                    3Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    13
  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
  3Q LOSS MUTATED       0                         4    11
  3Q LOSS WILD-TYPE     3                         5    32
D44V5, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                  11                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"

Clustering(45) Variable = 4P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    9 20
  4P LOSS WILD-TYPE 12 14
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               29                26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               20                14 
$`4P LOSS MUTATED`
TCGA-N6-A4VE TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ 
        9.57        19.30        52.31         4.67        59.38        18.08 
TCGA-N5-A4RM TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
        4.87        50.17        14.70        11.87        32.19        19.63 
TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S 
       51.75         0.26        13.74        25.68        18.81        12.20 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-NA-A5I1 
       54.97        35.80        80.78        27.55         6.67        88.11 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
       23.47         5.49         5.49        14.53        12.43 

$`4P LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       34.62        81.70         3.68        27.25        20.09        25.18 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A59B 
       22.52        29.95        67.13        17.16        25.35        27.19 
TCGA-N8-A4PI TCGA-N8-A4PN TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       26.63        26.70        21.93        67.17        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-NF-A4WU TCGA-NF-A4WX 
      140.35         3.75        17.79        10.42         9.80        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VW 
        2.66        31.20 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.26              2.66 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            88.11            140.35 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            18.81             23.85 
[1] "0.3 - 88.1 (18.8)"  "2.7 - 140.3 (23.9)"
[1] "hr=" "1.4"
D45V2, continuous
D45V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   16 12
  4P LOSS WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16   12
  4P LOSS WILD-TYPE   13   12
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               16                13
  YES              12                12
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  4P LOSS MUTATED                                                                    15
  4P LOSS WILD-TYPE                                                                   9
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  4P LOSS MUTATED                                                12
  4P LOSS WILD-TYPE                                               7
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  4P LOSS MUTATED                                              3
  4P LOSS WILD-TYPE                                           10
D45V4, multiclass
                                                                     clus
vv                                                                    4P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              15
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  12
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      3
                                                                     clus
vv                                                                    4P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 9
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       10
[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
  4P LOSS MUTATED       2                         4    24
  4P LOSS WILD-TYPE     1                         5    19
D45V5, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                  24                19
[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(46) Variable = 4Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   10 23
  4Q LOSS WILD-TYPE 11 11
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               33                22 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               23                11 
$`4Q LOSS MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF 
        9.57        20.09        19.30        52.31         4.67        59.38 
TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F 
       18.08         4.87        22.52        50.17        14.70        11.87 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N7-A4Y5 TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PQ 
       32.19        19.63         0.26        13.74        25.68        18.81 
TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QW 
       12.20        67.17        54.97        35.80       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       27.55         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4WX TCGA-NG-A4VU TCGA-N7-A4Y8 
       14.86        14.53        12.43 

$`4Q LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PM TCGA-ND-A4WC TCGA-N5-A4RS 
       34.62        81.70         3.68        27.25        25.18        29.95 
TCGA-N5-A4RV TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI 
       67.13        17.16        51.75        25.35        27.19        26.63 
TCGA-N8-A4PN TCGA-N9-A4PZ TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QY TCGA-NA-A4R0 
       26.70        21.93        19.86        15.81         3.75        17.79 
TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW 
        9.80         2.66         5.49        31.20 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.26              2.66 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           140.35             81.70 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           19.300            25.265 
[1] "0.3 - 140.3 (19.3)" "2.7 - 81.7 (25.3)" 
[1] "hr=" "1.3"
D46V2, continuous
D46V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   19 13
  4Q LOSS WILD-TYPE 10 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     19   13
  4Q LOSS WILD-TYPE   10   11
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               19                10
  YES              13                11
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  4Q LOSS MUTATED                                                                    15
  4Q LOSS WILD-TYPE                                                                   9
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  4Q LOSS MUTATED                                                14
  4Q LOSS WILD-TYPE                                               5
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  4Q LOSS MUTATED                                              5
  4Q LOSS WILD-TYPE                                            8
D46V4, multiclass
                                                                     clus
vv                                                                    4Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              15
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  14
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      5
                                                                     clus
vv                                                                    4Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 9
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     5
  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
  4Q LOSS MUTATED       2                         8    23
  4Q LOSS WILD-TYPE     1                         1    20
D46V5, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               8                 1
  WHITE                                  23                20
[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(47) Variable = 5P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    2  7
  5P LOSS WILD-TYPE 19 27
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                46 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                27 
$`5P LOSS MUTATED`
TCGA-N5-A4RN TCGA-N8-A4PM TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N6-A4VC TCGA-N9-A4Q8 
       34.62        27.25         4.67         4.87        19.63        15.81 
TCGA-NA-A4R1 TCGA-ND-A4WA TCGA-N7-A4Y8 
        6.67        23.47        12.43 

$`5P LOSS WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM 
       81.70         3.68         9.57        20.09        25.18        19.30 
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU 
       52.31        59.38        18.08        22.52        29.95        50.17 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N6-A4VG 
       67.13        14.70        11.87        32.19        17.16        51.75 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN 
       25.35         0.26        27.19        26.63        13.74        26.70 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       25.68        18.81        12.20        21.93        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY 
       35.80        19.86       140.35        80.78        27.55         3.75 
TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX 
       17.79        88.11        10.42         5.49         9.80        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        2.66         5.49        14.53        31.20 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             4.67              0.26 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            34.62            140.35 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           15.810            22.225 
[1] "4.7 - 34.6 (15.8)"  "0.3 - 140.3 (22.2)"
[1] "hr=" "2.1"
D47V2, continuous
D47V3, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    6  2
  5P LOSS WILD-TYPE 23 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    2
  5P LOSS WILD-TYPE   23   22
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                6                23
  YES               2                22
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  5P LOSS MUTATED                                                                     3
  5P LOSS WILD-TYPE                                                                  21
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  5P LOSS MUTATED                                                 4
  5P LOSS WILD-TYPE                                              15
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  5P LOSS MUTATED                                              2
  5P LOSS WILD-TYPE                                           11
D47V4, multiclass
                                                                     clus
vv                                                                    5P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   4
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      2
                                                                     clus
vv                                                                    5P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                21
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    15
  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
  5P LOSS MUTATED       1                         1     7
  5P LOSS WILD-TYPE     2                         8    36
D47V5, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 8
  WHITE                                   7                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"

Clustering(48) Variable = 5Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    7 11
  5Q LOSS WILD-TYPE 14 23
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               18                37 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               11                23 
$`5Q LOSS MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N5-A4RD TCGA-N5-A4RM 
       34.62        81.70        27.25        20.09         4.67         4.87 
TCGA-N7-A4Y5 TCGA-N8-A4PO TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q8 
        0.26        25.68        21.93        67.17        35.80        15.81 
TCGA-NA-A4R1 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-N7-A4Y8 
        6.67        23.47         9.80         2.66        14.53        12.43 

$`5Q LOSS WILD-TYPE`
TCGA-N6-A4VD TCGA-N6-A4VE TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RF 
        3.68         9.57        25.18        19.30        52.31        59.38 
TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       18.08        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-A4Y0 
       11.87        32.19        19.63        17.16        51.75        25.35 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S 
       27.19        26.63        13.74        26.70        18.81        12.20 
TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY 
       54.97        19.86       140.35        80.78        27.55         3.75 
TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A5CP 
       17.79        88.11        10.42         5.49        14.86         5.49 
TCGA-NG-A4VW 
       31.20 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.26              3.68 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            81.70            140.35 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            17.95             22.52 
[1] "0.3 - 81.7 (17.9)"  "3.7 - 140.3 (22.5)"
[1] "hr=" "1.3"
D48V2, continuous
D48V3, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   11  5
  5Q LOSS WILD-TYPE 18 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11    5
  5Q LOSS WILD-TYPE   18   19
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               11                18
  YES               5                19
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  5Q LOSS MUTATED                                                                     7
  5Q LOSS WILD-TYPE                                                                  17
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  5Q LOSS MUTATED                                                 7
  5Q LOSS WILD-TYPE                                              12
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  5Q LOSS MUTATED                                              4
  5Q LOSS WILD-TYPE                                            9
D48V4, multiclass
                                                                     clus
vv                                                                    5Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      4
                                                                     clus
vv                                                                    5Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    12
  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
  5Q LOSS MUTATED       1                         4    13
  5Q LOSS WILD-TYPE     2                         5    30
D48V5, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               4                 5
  WHITE                                  13                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(49) Variable = 6P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    4  1
  6P LOSS WILD-TYPE 17 33
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                50 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                33 
$`6P LOSS MUTATED`
TCGA-QM-A5NM TCGA-N5-A59F TCGA-N6-A4VG TCGA-N8-A4PQ TCGA-NA-A4QV 
       19.30        11.87        51.75        18.81       140.35 

$`6P LOSS 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-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
       25.18        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-N6-A4V9 
       22.52        29.95        50.17        67.13        14.70        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-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       13.74        26.70        25.68        12.20        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX 
       54.97        35.80        19.86        15.81        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-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
        5.49         9.80        14.86         2.66         5.49        14.53 
TCGA-NG-A4VW TCGA-N7-A4Y8 
       31.20        12.43 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            11.87              0.26 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           140.35             88.11 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            19.30             21.01 
[1] "11.9 - 140.3 (19.3)" "0.3 - 88.1 (21.0)"  
[1] "hr=" "4.7"
D49V2, continuous
D49V3, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    2  3
  6P LOSS WILD-TYPE 27 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    3
  6P LOSS WILD-TYPE   27   21
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                2                27
  YES               3                21
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  6P LOSS MUTATED                                                                     3
  6P LOSS WILD-TYPE                                                                  21
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  6P LOSS MUTATED                                                 1
  6P LOSS WILD-TYPE                                              18
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  6P LOSS MUTATED                                              1
  6P LOSS WILD-TYPE                                           12
D49V4, multiclass
                                                                     clus
vv                                                                    6P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   1
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      1
                                                                     clus
vv                                                                    6P LOSS 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
  6P LOSS MUTATED       0                         2     3
  6P LOSS WILD-TYPE     3                         7    40
D49V5, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               2                 7
  WHITE                                   3                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(50) Variable = 6Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    4  2
  6Q LOSS WILD-TYPE 17 32
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6                49 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                32 
$`6Q LOSS MUTATED`
TCGA-N5-A59F TCGA-N6-A4VG TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-NA-A4QV TCGA-NA-A4QY 
       11.87        51.75        26.70        18.81       140.35         3.75 

$`6Q LOSS 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ 
       25.18        19.30        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-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B 
       32.19        19.63        17.16        25.35         0.26        27.19 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       26.63        13.74        25.68        12.20        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX 
       54.97        35.80        19.86        15.81        80.78        27.55 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       17.79         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        9.80        14.86         2.66         5.49        14.53        31.20 
TCGA-N7-A4Y8 
       12.43 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             3.75              0.26 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           140.35             88.11 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           22.755            20.090 
[1] "3.8 - 140.3 (22.8)" "0.3 - 88.1 (20.1)" 
[1] "hr=" "2.4"
D50V2, continuous
D50V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    4  3
  6Q LOSS WILD-TYPE 25 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    3
  6Q LOSS WILD-TYPE   25   21
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                4                25
  YES               3                21
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  6Q LOSS MUTATED                                                                     3
  6Q LOSS WILD-TYPE                                                                  21
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  6Q LOSS MUTATED                                                 2
  6Q LOSS WILD-TYPE                                              17
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  6Q LOSS MUTATED                                              2
  6Q LOSS WILD-TYPE                                           11
D50V4, multiclass
                                                                     clus
vv                                                                    6Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   2
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      2
                                                                     clus
vv                                                                    6Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                21
  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
  6Q LOSS MUTATED       1                         2     4
  6Q LOSS WILD-TYPE     2                         7    39
D50V5, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               2                 7
  WHITE                                   4                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(51) Variable = 7P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    6  7
  7P LOSS WILD-TYPE 15 27
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13                42 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                7                27 
$`7P LOSS MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VF 
        9.57        27.25        14.70        11.87        19.63        17.16 
TCGA-N7-A4Y5 TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QW 
        0.26        25.68        18.81        54.97        15.81        80.78 
TCGA-NF-A4WU 
        9.80 

$`7P LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62        81.70         3.68        20.09        25.18        19.30 
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-N6-A4V9 TCGA-N6-A4VG TCGA-N7-A4Y0 
       29.95        50.17        67.13        32.19        51.75        25.35 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A56S TCGA-N9-A4PZ 
       27.19        26.63        13.74        26.70        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY 
       67.17        35.80        19.86       140.35        27.55         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       17.79         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
       14.86         2.66         5.49        14.53        31.20        12.43 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.26              2.66 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            80.78            140.35 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           17.160            22.995 
[1] "0.3 - 80.8 (17.2)"  "2.7 - 140.3 (23.0)"
[1] "hr=" "1.1"
D51V2, continuous
D51V3, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    8  5
  7P LOSS WILD-TYPE 21 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8    5
  7P LOSS WILD-TYPE   21   19
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                8                21
  YES               5                19
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  7P LOSS MUTATED                                                                     7
  7P LOSS WILD-TYPE                                                                  17
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  7P LOSS MUTATED                                                 4
  7P LOSS WILD-TYPE                                              15
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  7P LOSS MUTATED                                              2
  7P LOSS WILD-TYPE                                           11
D51V4, multiclass
                                                                     clus
vv                                                                    7P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   4
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      2
                                                                     clus
vv                                                                    7P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    15
  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
  7P LOSS MUTATED       0                         2    11
  7P LOSS WILD-TYPE     3                         7    32
D51V5, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               2                 7
  WHITE                                  11                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"

Clustering(52) Variable = 7Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    4  8
  7Q LOSS WILD-TYPE 17 26
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               12                43 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                8                26 
$`7Q LOSS MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC 
        9.57        27.25        50.17        14.70        11.87        19.63 
TCGA-N7-A4Y5 TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4Q8 TCGA-ND-A4W6 TCGA-NF-A4WU 
        0.26        25.68        18.81        15.81        10.42         9.80 

$`7Q LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62        81.70         3.68        20.09        25.18        19.30 
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-A4RV TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       29.95        67.13        32.19        17.16        51.75        25.35 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A56S TCGA-N9-A4PZ 
       27.19        26.63        13.74        26.70        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW 
       67.17        54.97        35.80        19.86       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WA 
       27.55         3.75        17.79         6.67        88.11        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 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.26              2.66 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            50.17            140.35 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           15.255            23.470 
[1] "0.3 - 50.2 (15.3)"  "2.7 - 140.3 (23.5)"
[1] "hr=" "1.9"
D52V2, continuous
D52V3, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    9  3
  7Q LOSS WILD-TYPE 20 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9    3
  7Q LOSS WILD-TYPE   20   21
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                9                20
  YES               3                21
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  7Q LOSS MUTATED                                                                     4
  7Q LOSS WILD-TYPE                                                                  20
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  7Q LOSS MUTATED                                                 5
  7Q LOSS WILD-TYPE                                              14
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  7Q LOSS MUTATED                                              3
  7Q LOSS WILD-TYPE                                           10
D52V4, multiclass
                                                                     clus
vv                                                                    7Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               4
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      3
                                                                     clus
vv                                                                    7Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                20
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    14
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       10
[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
  7Q LOSS MUTATED       0                         3     9
  7Q LOSS WILD-TYPE     3                         6    34
D52V5, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                   9                34
[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(53) Variable = 8P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    7 16
  8P LOSS WILD-TYPE 14 18
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               23                32 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                18 
$`8P LOSS MUTATED`
TCGA-N5-A4RN TCGA-N8-A4PP TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F 
       34.62        20.09        22.52        50.17        14.70        11.87 
TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A56S 
       19.63        51.75         0.26        26.70        25.68        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-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-NG-A4VU 
       27.55         3.75        17.79        88.11        14.53 

$`8P LOSS WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-ND-A4WC TCGA-QM-A5NM 
       81.70         3.68         9.57        27.25        25.18        19.30 
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RS 
       52.31         4.67        59.38        18.08         4.87        29.95 
TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI 
       67.13        32.19        17.16        25.35        27.19        26.63 
TCGA-N8-A4PL TCGA-N8-A4PQ TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4R1 TCGA-ND-A4W6 
       13.74        18.81       140.35        80.78         6.67        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-A4VW TCGA-N7-A4Y8 
       31.20        12.43 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.26              2.66 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            88.11            140.35 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           21.930            19.055 
[1] "0.3 - 88.1 (21.9)"  "2.7 - 140.3 (19.1)"
[1] "hr=" "1.1"
D53V2, continuous
D53V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   12 11
  8P LOSS WILD-TYPE 17 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     12   11
  8P LOSS WILD-TYPE   17   13
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               12                17
  YES              11                13
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  8P LOSS MUTATED                                                                    12
  8P LOSS WILD-TYPE                                                                  12
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  8P LOSS MUTATED                                                 6
  8P LOSS WILD-TYPE                                              13
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  8P LOSS MUTATED                                              6
  8P LOSS WILD-TYPE                                            7
D53V4, multiclass
                                                                     clus
vv                                                                    8P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              12
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   6
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      6
                                                                     clus
vv                                                                    8P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                12
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    13
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        7
[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
  8P LOSS MUTATED       1                         6    17
  8P LOSS WILD-TYPE     2                         3    26
D53V5, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               6                 3
  WHITE                                  17                26
[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(54) Variable = 8Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    3  6
  8Q LOSS WILD-TYPE 18 28
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9                46 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                6                28 
$`8Q LOSS MUTATED`
TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A59F TCGA-N6-A4VG TCGA-N8-A56S TCGA-N9-A4PZ 
       22.52        50.17        11.87        51.75        12.20        21.93 
TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4QX 
       54.97        19.86        27.55 

$`8Q LOSS 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ 
       25.18        19.30        52.31         4.67        59.38        18.08 
TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC 
        4.87        29.95        67.13        14.70        32.19        19.63 
TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       17.16        25.35         0.26        27.19        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q8 
       26.70        25.68        18.81        67.17        35.80        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
      140.35        80.78         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-NG-A4VW TCGA-N7-A4Y8 
        5.49        14.53        31.20        12.43 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            11.87              0.26 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            54.97            140.35 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           22.520            19.465 
[1] "11.9 - 55.0 (22.5)" "0.3 - 140.3 (19.5)"
[1] "hr=" "1"  
D54V2, continuous
D54V3, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  7
  8Q LOSS WILD-TYPE 27 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    7
  8Q LOSS WILD-TYPE   27   17
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                2                27
  YES               7                17
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  8Q LOSS MUTATED                                                                     5
  8Q LOSS WILD-TYPE                                                                  19
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  8Q LOSS MUTATED                                                 1
  8Q LOSS WILD-TYPE                                              18
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  8Q LOSS MUTATED                                              3
  8Q LOSS WILD-TYPE                                           10
D54V4, multiclass
                                                                     clus
vv                                                                    8Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               5
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   1
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      3
                                                                     clus
vv                                                                    8Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                19
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    18
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       10
[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
  8Q LOSS MUTATED       0                         3     6
  8Q LOSS WILD-TYPE     3                         6    37
D54V5, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                   6                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(55) Variable = 9P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   15 19
  9P LOSS WILD-TYPE  6 15
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               34                21 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19                15 
$`9P LOSS MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PM TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RM 
        9.57        27.25        19.30        52.31        18.08         4.87 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N6-A4VG 
       67.13        14.70        11.87        32.19        17.16        51.75 
TCGA-N7-A4Y5 TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 
        0.26        26.70        25.68        18.81        12.20        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       54.97        35.80        19.86        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4WA TCGA-NF-A4WX 
       27.55         3.75        17.79         6.67        23.47        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
        2.66         5.49        14.53        12.43 

$`9P LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-N5-A4RD 
       34.62        81.70         3.68        20.09        25.18         4.67 
TCGA-N5-A4RF TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N6-A4VC TCGA-N7-A4Y0 
       59.38        22.52        29.95        50.17        19.63        25.35 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N9-A4PZ TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.19        26.63        13.74        21.93        88.11        10.42 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NG-A4VW 
        5.49         9.80        31.20 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.26              3.68 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           140.35             88.11 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           18.445            25.180 
[1] "0.3 - 140.3 (18.4)" "3.7 - 88.1 (25.2)" 
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   20 14
  9P LOSS WILD-TYPE  9 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     20   14
  9P LOSS WILD-TYPE    9   10
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               20                 9
  YES              14                10
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  9P LOSS MUTATED                                                                    17
  9P LOSS WILD-TYPE                                                                   7
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  9P LOSS MUTATED                                                14
  9P LOSS WILD-TYPE                                               5
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  9P LOSS MUTATED                                              4
  9P LOSS WILD-TYPE                                            9
D55V4, multiclass
                                                                     clus
vv                                                                    9P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  14
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      4
                                                                     clus
vv                                                                    9P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     5
  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
  9P LOSS MUTATED       2                         7    25
  9P LOSS WILD-TYPE     1                         2    18
D55V5, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               7                 2
  WHITE                                  25                18
[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(56) Variable = 9Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   18 21
  9Q LOSS WILD-TYPE  3 13
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               39                16 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               21                13 
$`9Q LOSS MUTATED`
TCGA-N5-A4RN TCGA-N6-A4VE TCGA-N8-A4PM TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RF 
       34.62         9.57        27.25        19.30        52.31        59.38 
TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       18.08         4.87        67.13        14.70        11.87        32.19 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PN TCGA-N8-A4PO 
       17.16        51.75         0.26        27.19        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-A4R1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WX TCGA-NF-A4X2 
       17.79         6.67        10.42        23.47        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
        5.49        14.53        12.43 

$`9Q LOSS WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-N5-A4RD TCGA-N5-A4RO 
       81.70         3.68        20.09        25.18         4.67        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N6-A4VC TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PL 
       29.95        50.17        19.63        25.35        26.63        13.74 
TCGA-NA-A5I1 TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NG-A4VW 
       88.11         5.49         9.80        31.20 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.26              3.68 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           140.35             88.11 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            19.30             23.85 
[1] "0.3 - 140.3 (19.3)" "3.7 - 88.1 (23.9)" 
[1] "hr=" "1.4"
D56V2, continuous
D56V3, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   22 16
  9Q LOSS WILD-TYPE  7  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     22   16
  9Q LOSS WILD-TYPE    7    8
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               22                 7
  YES              16                 8
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  9Q LOSS MUTATED                                                                    18
  9Q LOSS WILD-TYPE                                                                   6
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  9Q LOSS MUTATED                                                15
  9Q LOSS WILD-TYPE                                               4
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  9Q LOSS MUTATED                                              7
  9Q LOSS WILD-TYPE                                            6
D56V4, multiclass
                                                                     clus
vv                                                                    9Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS              18
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                  15
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      7
                                                                     clus
vv                                                                    9Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 6
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     4
  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
  9Q LOSS MUTATED       2                         8    29
  9Q LOSS WILD-TYPE     1                         1    14
D56V5, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               8                 1
  WHITE                                  29                14
[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(57) Variable = 10P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    9 15
  10P LOSS WILD-TYPE 12 19
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                24                 31 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                15                 19 
$`10P LOSS MUTATED`
TCGA-N5-A4RN TCGA-N6-A4VE TCGA-N8-A4PM TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD 
       34.62         9.57        27.25        19.30        52.31         4.67 
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 
        4.87        22.52        50.17        67.13        14.70        32.19 
TCGA-N6-A4VF TCGA-N8-A4PO TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       17.16        25.68        21.93        67.17        35.80        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-N7-A4Y8 
       15.81        80.78        17.79         6.67        88.11        12.43 

$`10P LOSS WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-N5-A4RF TCGA-N5-A4RJ 
       81.70         3.68        20.09        25.18        59.38        18.08 
TCGA-N5-A4RS TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       29.95        11.87        19.63        51.75        25.35         0.26 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S 
       27.19        26.63        13.74        26.70        18.81        12.20 
TCGA-N9-A4Q3 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY TCGA-ND-A4W6 TCGA-ND-A4WA 
       54.97       140.35        27.55         3.75        10.42        23.47 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
        5.49         9.80        14.86         2.66         5.49        14.53 
TCGA-NG-A4VW 
       31.20 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              4.67               0.26 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             88.11             140.35 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            22.225             19.630 
[1] "4.7 - 88.1 (22.2)"  "0.3 - 140.3 (19.6)"
[1] "hr=" "1.2"
D57V2, continuous
D57V3, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   10 12
  10P LOSS WILD-TYPE 19 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     10   12
  10P LOSS WILD-TYPE   19   12
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                10                 19
  YES               12                 12
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  10P LOSS MUTATED                                                                    12
  10P LOSS WILD-TYPE                                                                  12
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  10P LOSS MUTATED                                                 7
  10P LOSS WILD-TYPE                                              12
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  10P LOSS MUTATED                                              5
  10P LOSS WILD-TYPE                                            8
D57V4, multiclass
                                                                     clus
vv                                                                    10P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               12
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       5
                                                                     clus
vv                                                                    10P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 12
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     12
  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
  10P LOSS MUTATED       0                         6    18
  10P LOSS WILD-TYPE     3                         3    25
D57V5, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                6                  3
  WHITE                                   18                 25
[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(58) Variable = 10Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    5 15
  10Q LOSS WILD-TYPE 16 19
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                20                 35 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                 19 
$`10Q LOSS MUTATED`
TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM 
        9.57        27.25        52.31         4.67        18.08         4.87 
TCGA-N5-A4RO TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N8-A4PO TCGA-N9-A4PZ TCGA-N9-A4Q4 
       22.52        32.19        17.16        25.68        21.93        35.80 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
       19.86        15.81        27.55        17.79         6.67        88.11 
TCGA-NF-A5CP TCGA-N7-A4Y8 
        5.49        12.43 

$`10Q LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62        81.70         3.68        20.09        25.18        19.30 
TCGA-N5-A4RF TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
       59.38        29.95        50.17        67.13        14.70        11.87 
TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI 
       19.63        51.75        25.35         0.26        27.19        26.63 
TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       13.74        26.70        18.81        12.20        67.17        54.97 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
      140.35        80.78         3.75        10.42        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW 
        9.80        14.86         2.66        14.53        31.20 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              4.67               0.26 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             88.11             140.35 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             18.97              23.47 
[1] "4.7 - 88.1 (19.0)"  "0.3 - 140.3 (23.5)"
[1] "hr=" "1.6"
D58V2, continuous
D58V3, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    9  9
  10Q LOSS WILD-TYPE 20 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      9    9
  10Q LOSS WILD-TYPE   20   15
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 9                 20
  YES                9                 15
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  10Q LOSS MUTATED                                                                    11
  10Q LOSS WILD-TYPE                                                                  13
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  10Q LOSS MUTATED                                                 7
  10Q LOSS WILD-TYPE                                              12
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  10Q LOSS MUTATED                                              2
  10Q LOSS WILD-TYPE                                           11
D58V4, multiclass
                                                                     clus
vv                                                                    10Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       2
                                                                     clus
vv                                                                    10Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     12
  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
  10Q LOSS MUTATED       0                         5    15
  10Q LOSS WILD-TYPE     3                         4    28
D58V5, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                5                  4
  WHITE                                   15                 28
[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(59) Variable = 11P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    7 21
  11P LOSS WILD-TYPE 14 13
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                28                 27 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                21                 13 
$`11P LOSS MUTATED`
TCGA-N8-A4PM TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N5-A4RO 
       27.25        19.30        52.31         4.67         4.87        22.52 
TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VG 
       50.17        14.70        11.87        32.19        19.63        51.75 
TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q4 
        0.26        26.63        13.74        12.20        21.93        35.80 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       17.79         6.67        88.11        10.42        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP TCGA-N7-A4Y8 
        9.80        14.86         5.49        12.43 

$`11P LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PP TCGA-ND-A4WC 
       34.62        81.70         3.68         9.57        20.09        25.18 
TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N6-A4VF TCGA-N7-A4Y0 
       59.38        18.08        29.95        67.13        17.16        25.35 
TCGA-N7-A59B TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       27.19        26.70        25.68        18.81        67.17        54.97 
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-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW 
        2.66        14.53        31.20 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.26               2.66 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             88.11             140.35 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            16.325             25.680 
[1] "0.3 - 88.1 (16.3)"  "2.7 - 140.3 (25.7)"
[1] "hr=" "2.3"
D59V2, continuous
D59V3, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   17  9
  11P LOSS WILD-TYPE 12 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     17    9
  11P LOSS WILD-TYPE   12   15
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                17                 12
  YES                9                 15
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  11P LOSS MUTATED                                                                    11
  11P LOSS WILD-TYPE                                                                  13
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  11P LOSS MUTATED                                                13
  11P LOSS WILD-TYPE                                               6
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  11P LOSS MUTATED                                              4
  11P LOSS WILD-TYPE                                            9
D59V4, multiclass
                                                                     clus
vv                                                                    11P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   13
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       4
                                                                     clus
vv                                                                    11P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      6
  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
  11P LOSS MUTATED       1                         5    21
  11P LOSS WILD-TYPE     2                         4    22
D59V5, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                5                  4
  WHITE                                   21                 22
[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(60) Variable = 11Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    8 18
  11Q LOSS WILD-TYPE 13 16
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                 29 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                18                 16 
$`11Q LOSS MUTATED`
TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO 
       19.30        52.31         4.67        59.38         4.87        22.52 
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-N8-A4PL TCGA-N8-A4PO TCGA-N9-A4PZ TCGA-N9-A4Q4 
       51.75         0.26        13.74        25.68        21.93        35.80 
TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX 
       17.79        88.11        10.42        23.47         5.49        14.86 
TCGA-NF-A5CP TCGA-N7-A4Y8 
        5.49        12.43 

$`11Q LOSS 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-N5-A4RJ TCGA-N5-A4RS TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A59B 
       25.18        18.08        29.95        17.16        25.35        27.19 
TCGA-N8-A4PI TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       26.63        26.70        18.81        12.20        67.17        54.97 
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-A4R1 TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW 
        6.67         9.80         2.66        14.53        31.20 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.26               2.66 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             88.11             140.35 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            19.465             25.180 
[1] "0.3 - 88.1 (19.5)"  "2.7 - 140.3 (25.2)"
[1] "hr=" "1.4"
D60V2, continuous
D60V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   14 10
  11Q LOSS WILD-TYPE 15 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     14   10
  11Q LOSS WILD-TYPE   15   14
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                14                 15
  YES               10                 14
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  11Q LOSS MUTATED                                                                     9
  11Q LOSS WILD-TYPE                                                                  15
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  11Q LOSS MUTATED                                                12
  11Q LOSS WILD-TYPE                                               7
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  11Q LOSS MUTATED                                              5
  11Q LOSS WILD-TYPE                                            8
D60V4, multiclass
                                                                     clus
vv                                                                    11Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                9
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   12
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       5
                                                                     clus
vv                                                                    11Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 15
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      7
  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
  11Q LOSS MUTATED       1                         5    19
  11Q LOSS WILD-TYPE     2                         4    24
D60V5, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                5                  4
  WHITE                                   19                 24
[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(61) Variable = 12P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    6  7
  12P LOSS WILD-TYPE 15 27
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                13                 42 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 7                 27 
$`12P LOSS MUTATED`
TCGA-N8-A4PP TCGA-N5-A59F TCGA-N6-A4VG TCGA-N8-A4PI TCGA-N8-A4PN TCGA-N8-A4PO 
       20.09        11.87        51.75        26.63        26.70        25.68 
TCGA-N8-A4PQ TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY 
       18.81        15.81       140.35        80.78        27.55         3.75 
TCGA-NA-A4R1 
        6.67 

$`12P LOSS WILD-TYPE`
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-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
       19.30        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-N6-A4V9 
       22.52        29.95        50.17        67.13        14.70        32.19 
TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL 
       19.63        17.16        25.35         0.26        27.19        13.74 
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-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-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
       14.86         2.66         5.49        14.53        31.20        12.43 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              3.75               0.26 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            140.35              88.11 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            25.680             19.745 
[1] "3.8 - 140.3 (25.7)" "0.3 - 88.1 (19.7)" 
[1] "hr=" "1.4"
D61V2, continuous
D61V3, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    6  7
  12P LOSS WILD-TYPE 23 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6    7
  12P LOSS WILD-TYPE   23   17
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 6                 23
  YES                7                 17
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  12P LOSS MUTATED                                                                     6
  12P LOSS WILD-TYPE                                                                  18
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  12P LOSS MUTATED                                                 4
  12P LOSS WILD-TYPE                                              15
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  12P LOSS MUTATED                                              3
  12P LOSS WILD-TYPE                                           10
D61V4, multiclass
                                                                     clus
vv                                                                    12P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                6
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    4
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       3
                                                                     clus
vv                                                                    12P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 18
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     15
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        10
[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
  12P LOSS MUTATED       0                         4     9
  12P LOSS WILD-TYPE     3                         5    34
D61V5, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                4                  5
  WHITE                                    9                 34
[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(62) Variable = 12Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    4  9
  12Q LOSS WILD-TYPE 17 25
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                13                 42 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                 25 
$`12Q LOSS MUTATED`
TCGA-N8-A4PP TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VG TCGA-N8-A4PI TCGA-N8-A4PO 
       20.09        14.70        11.87        51.75        26.63        25.68 
TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NF-A4WU 
       15.81        80.78        27.55         3.75         6.67         9.80 
TCGA-N7-A4Y8 
       12.43 

$`12Q LOSS WILD-TYPE`
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-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
       19.30        52.31         4.67        59.38        18.08         4.87 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VC 
       22.52        29.95        50.17        67.13        32.19        19.63 
TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN 
       17.16        25.35         0.26        27.19        13.74        26.70 
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-NA-A4QV TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
       19.86       140.35        17.79        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 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              3.75               0.26 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             80.78             140.35 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            15.810             22.225 
[1] "3.8 - 80.8 (15.8)"  "0.3 - 140.3 (22.2)"
[1] "hr=" "1.5"
D62V2, continuous
D62V3, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    8  6
  12Q LOSS WILD-TYPE 21 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8    6
  12Q LOSS WILD-TYPE   21   18
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 8                 21
  YES                6                 18
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  12Q LOSS MUTATED                                                                     7
  12Q LOSS WILD-TYPE                                                                  17
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  12Q LOSS MUTATED                                                 5
  12Q LOSS WILD-TYPE                                              14
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  12Q LOSS MUTATED                                              2
  12Q LOSS WILD-TYPE                                           11
D62V4, multiclass
                                                                     clus
vv                                                                    12Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       2
                                                                     clus
vv                                                                    12Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     14
  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
  12Q LOSS MUTATED       1                         3    10
  12Q LOSS WILD-TYPE     2                         6    33
D62V5, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                   10                 33
[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(63) Variable = 13Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   11 14
  13Q LOSS WILD-TYPE 10 20
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                25                 30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                 20 
$`13Q LOSS MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RD 
       34.62        81.70         9.57        20.09        19.30         4.67 
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4VF TCGA-N6-A4VG 
        4.87        22.52        50.17        67.13        17.16        51.75 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q7 
       27.19        26.63        25.68        12.20        21.93        19.86 
TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4X2 
      140.35        27.55        17.79         5.49         9.80         2.66 
TCGA-NF-A5CP 
        5.49 

$`13Q LOSS WILD-TYPE`
TCGA-N6-A4VD TCGA-N8-A4PM TCGA-ND-A4WC TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ 
        3.68        27.25        25.18        52.31        59.38        18.08 
TCGA-N5-A4RS TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N7-A4Y0 
       29.95        14.70        11.87        32.19        19.63        25.35 
TCGA-N7-A4Y5 TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
        0.26        13.74        26.70        18.81        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 
       35.80        15.81        80.78         3.75         6.67        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WX TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
       10.42        23.47        14.86        14.53        31.20        12.43 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              2.66               0.26 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            140.35              88.11 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             20.09              21.55 
[1] "2.7 - 140.3 (20.1)" "0.3 - 88.1 (21.5)" 
[1] "hr=" "1.1"
D63V2, continuous
D63V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   14 10
  13Q LOSS WILD-TYPE 15 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     14   10
  13Q LOSS WILD-TYPE   15   14
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                14                 15
  YES               10                 14
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  13Q LOSS MUTATED                                                                    11
  13Q LOSS WILD-TYPE                                                                  13
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  13Q LOSS MUTATED                                                 8
  13Q LOSS WILD-TYPE                                              11
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  13Q LOSS MUTATED                                              7
  13Q LOSS WILD-TYPE                                            6
D63V4, multiclass
                                                                     clus
vv                                                                    13Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    8
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       7
                                                                     clus
vv                                                                    13Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     11
  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
  13Q LOSS MUTATED       1                         4    21
  13Q LOSS WILD-TYPE     2                         5    22
D63V5, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                4                  5
  WHITE                                   21                 22
[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(64) Variable = 14Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    7 19
  14Q LOSS WILD-TYPE 14 15
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                26                 29 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                 15 
$`14Q LOSS MUTATED`
TCGA-N5-A4RT TCGA-N8-A4PP TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM 
       81.70        20.09        52.31         4.67        18.08         4.87 
TCGA-N5-A4RO TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y5 
       22.52        14.70        11.87        19.63        51.75         0.26 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 
       26.63        13.74        25.68        18.81        12.20        67.17 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 
       35.80        19.86        27.55        17.79        88.11        10.42 
TCGA-ND-A4WA TCGA-NF-A4WU 
       23.47         9.80 

$`14Q LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62         3.68         9.57        27.25        25.18        19.30 
TCGA-N5-A4RF TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VF 
       59.38        29.95        50.17        67.13        32.19        17.16 
TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PN TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q8 
       25.35        27.19        26.70        21.93        54.97        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4WX 
      140.35        80.78         3.75         6.67         5.49        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
        2.66         5.49        14.53        31.20        12.43 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.26               2.66 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             88.11             140.35 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            19.745             25.180 
[1] "0.3 - 88.1 (19.7)"  "2.7 - 140.3 (25.2)"
[1] "hr=" "1.5"
D64V2, continuous
D64V3, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   17  8
  14Q LOSS WILD-TYPE 12 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     17    8
  14Q LOSS WILD-TYPE   12   16
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                17                 12
  YES                8                 16
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  14Q LOSS MUTATED                                                                    10
  14Q LOSS WILD-TYPE                                                                  14
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  14Q LOSS MUTATED                                                13
  14Q LOSS WILD-TYPE                                               6
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  14Q LOSS MUTATED                                              4
  14Q LOSS WILD-TYPE                                            9
D64V4, multiclass
                                                                     clus
vv                                                                    14Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               10
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   13
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       4
                                                                     clus
vv                                                                    14Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 14
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      6
  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
  14Q LOSS MUTATED       2                         7    18
  14Q LOSS WILD-TYPE     1                         2    25
D64V5, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                7                  2
  WHITE                                   18                 25
[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(65) Variable = 15Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   11 21
  15Q LOSS WILD-TYPE 10 13
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                32                 23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                 13 
$`15Q LOSS MUTATED`
TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RF 
       81.70         9.57        27.25        20.09        19.30        59.38 
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG 
        4.87        22.52        50.17        19.63        17.16        51.75 
TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S 
        0.26        26.63        13.74        25.68        18.81        12.20 
TCGA-N9-A4Q1 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A5I1 
       67.17        15.81        80.78        27.55         3.75        88.11 
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 

$`15Q LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N6-A4VD TCGA-ND-A4WC TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ 
       34.62         3.68        25.18        52.31         4.67        18.08 
TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N7-A4Y0 
       29.95        67.13        14.70        11.87        32.19        25.35 
TCGA-N7-A59B TCGA-N8-A4PN TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       27.19        26.70        21.93        54.97        35.80        19.86 
TCGA-NA-A4QV TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-NG-A4VW 
      140.35        17.79         6.67        10.42        31.20 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.26               3.68 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             88.11             140.35 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            19.055             25.350 
[1] "0.3 - 88.1 (19.1)"  "3.7 - 140.3 (25.4)"
[1] "hr=" "1.4"
D65V2, continuous
D65V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   21 12
  15Q LOSS WILD-TYPE  8 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     21   12
  15Q LOSS WILD-TYPE    8   12
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                21                  8
  YES               12                 12
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  15Q LOSS MUTATED                                                                    15
  15Q LOSS WILD-TYPE                                                                   9
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  15Q LOSS MUTATED                                                12
  15Q LOSS WILD-TYPE                                               7
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  15Q LOSS MUTATED                                              6
  15Q LOSS WILD-TYPE                                            7
D65V4, multiclass
                                                                     clus
vv                                                                    15Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               15
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   12
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       6
                                                                     clus
vv                                                                    15Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                  9
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                         7
[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
  15Q LOSS MUTATED       2                         3    27
  15Q LOSS WILD-TYPE     1                         6    16
D65V5, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                   27                 16
[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(66) Variable = 16P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   11 20
  16P LOSS WILD-TYPE 10 14
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                31                 24 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                20                 14 
$`16P LOSS MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N5-A4RA 
       34.62        81.70         9.57        27.25        20.09        52.31 
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F 
        4.67        59.38        22.52        50.17        14.70        11.87 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI 
       32.19        19.63        17.16         0.26        27.19        26.63 
TCGA-N8-A4PL TCGA-N8-A4PQ TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4R0 
       13.74        18.81        19.86        15.81        80.78        17.79 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU 
        6.67        88.11         5.49        14.86         2.66        14.53 
TCGA-N7-A4Y8 
       12.43 

$`16P LOSS WILD-TYPE`
TCGA-N6-A4VD TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RS 
        3.68        25.18        19.30        18.08         4.87        29.95 
TCGA-N5-A4RV TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A56S 
       67.13        51.75        25.35        26.70        25.68        12.20 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QX 
       21.93        67.17        54.97        35.80       140.35        27.55 
TCGA-NA-A4QY TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VW 
        3.75        10.42        23.47         9.80         5.49        31.20 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.26               3.68 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             88.11             140.35 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            18.810             25.265 
[1] "0.3 - 88.1 (18.8)"  "3.7 - 140.3 (25.3)"
[1] "hr=" "1.3"
D66V2, continuous
D66V3, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   18 12
  16P LOSS WILD-TYPE 11 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     18   12
  16P LOSS WILD-TYPE   11   12
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                18                 11
  YES               12                 12
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  16P LOSS MUTATED                                                                    12
  16P LOSS WILD-TYPE                                                                  12
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  16P LOSS MUTATED                                                11
  16P LOSS WILD-TYPE                                               8
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  16P LOSS MUTATED                                              9
  16P LOSS WILD-TYPE                                            4
D66V4, multiclass
                                                                     clus
vv                                                                    16P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               12
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   11
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       9
                                                                     clus
vv                                                                    16P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 12
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      8
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                         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"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         4    26
  16P LOSS WILD-TYPE     2                         5    17
D66V5, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                4                  5
  WHITE                                   26                 17
[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(67) Variable = 16Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   12 24
  16Q LOSS WILD-TYPE  9 10
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                36                 19 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                24                 10 
$`16Q LOSS MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N5-A4RA 
       34.62        81.70         9.57        27.25        20.09        52.31 
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A59E 
        4.67        59.38        18.08        22.52        50.17        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N7-A4Y5 TCGA-N7-A59B 
       11.87        32.19        19.63        17.16         0.26        27.19 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       26.63        13.74        26.70        18.81        19.86        15.81 
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-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
        5.49        14.86         2.66         5.49        14.53        12.43 

$`16Q LOSS WILD-TYPE`
TCGA-N6-A4VD TCGA-ND-A4WC TCGA-QM-A5NM TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RV 
        3.68        25.18        19.30         4.87        29.95        67.13 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       51.75        25.35        25.68        12.20        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-ND-A4WA TCGA-NF-A4WU 
       54.97        35.80       140.35        27.55        23.47         9.80 
TCGA-NG-A4VW 
       31.20 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.26               3.68 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             88.11             140.35 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            17.935             25.680 
[1] "0.3 - 88.1 (17.9)"  "3.7 - 140.3 (25.7)"
[1] "hr=" "1.8"
D67V2, continuous
D67V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   22 13
  16Q LOSS WILD-TYPE  7 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     22   13
  16Q LOSS WILD-TYPE    7   11
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                22                  7
  YES               13                 11
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  16Q LOSS MUTATED                                                                    13
  16Q LOSS WILD-TYPE                                                                  11
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  16Q LOSS MUTATED                                                14
  16Q LOSS WILD-TYPE                                               5
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  16Q LOSS MUTATED                                             10
  16Q LOSS WILD-TYPE                                            3
D67V4, multiclass
                                                                     clus
vv                                                                    16Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   14
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      10
                                                                     clus
vv                                                                    16Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                         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"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         5    30
  16Q LOSS WILD-TYPE     2                         4    13
D67V5, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                5                  4
  WHITE                                   30                 13
[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(68) Variable = 17P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   12 22
  17P LOSS WILD-TYPE  9 12
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                34                 21 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                22                 12 
$`17P LOSS MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VE TCGA-N8-A4PM TCGA-QM-A5NM TCGA-N5-A4RA 
       34.62        81.70         9.57        27.25        19.30        52.31 
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RU 
        4.67        59.38        18.08         4.87        22.52        50.17 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y5 
       14.70        11.87        32.19        19.63        51.75         0.26 
TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q8 
       25.68        12.20        21.93        54.97        35.80        15.81 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU 
       27.55         3.75        17.79        23.47         5.49         9.80 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
        2.66         5.49        14.53        12.43 

$`17P LOSS WILD-TYPE`
TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N6-A4VF 
        3.68        20.09        25.18        29.95        67.13        17.16 
TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ 
       25.35        27.19        26.63        13.74        26.70        18.81 
TCGA-N9-A4Q1 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4R1 TCGA-NA-A5I1 
       67.17        19.86       140.35        80.78         6.67        88.11 
TCGA-ND-A4W6 TCGA-NF-A4WX TCGA-NG-A4VW 
       10.42        14.86        31.20 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.26               3.68 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             81.70             140.35 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             18.69              25.35 
[1] "0.3 - 81.7 (18.7)"  "3.7 - 140.3 (25.4)"
[1] "hr=" "1.6"
D68V2, continuous
D68V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   19 13
  17P LOSS WILD-TYPE 10 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     19   13
  17P LOSS WILD-TYPE   10   11
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                19                 10
  YES               13                 11
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  17P LOSS MUTATED                                                                    13
  17P LOSS WILD-TYPE                                                                  11
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  17P LOSS MUTATED                                                14
  17P LOSS WILD-TYPE                                               5
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  17P LOSS MUTATED                                              7
  17P LOSS WILD-TYPE                                            6
D68V4, multiclass
                                                                     clus
vv                                                                    17P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   14
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       7
                                                                     clus
vv                                                                    17P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      5
  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
  17P LOSS MUTATED       1                         4    29
  17P LOSS WILD-TYPE     2                         5    14
D68V5, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                4                  5
  WHITE                                   29                 14
[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(69) Variable = 17Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    4 13
  17Q LOSS WILD-TYPE 17 21
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                 38 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                 21 
$`17Q LOSS MUTATED`
TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A59E 
       19.30        52.31         4.67         4.87        22.52        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N8-A4PO TCGA-N9-A4Q8 
       11.87        32.19        19.63        51.75        25.68        15.81 
TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
       27.55        17.79         5.49        14.53        12.43 

$`17Q LOSS 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-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV 
       25.18        59.38        18.08        29.95        50.17        67.13 
TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       17.16        25.35         0.26        27.19        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       26.70        18.81        12.20        21.93        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R1 
       35.80        19.86       140.35        80.78         3.75         6.67 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX 
       88.11        10.42        23.47         5.49         9.80        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VW 
        2.66        31.20 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              4.67               0.26 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             52.31             140.35 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            17.790             24.325 
[1] "4.7 - 52.3 (17.8)"  "0.3 - 140.3 (24.3)"
[1] "hr=" "1.9"
D69V2, continuous
D69V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    9  7
  17Q LOSS WILD-TYPE 20 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9    7
  17Q LOSS WILD-TYPE   20   17
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 9                 20
  YES                7                 17
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  17Q LOSS MUTATED                                                                     8
  17Q LOSS WILD-TYPE                                                                  16
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  17Q LOSS MUTATED                                                 7
  17Q LOSS WILD-TYPE                                              12
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  17Q LOSS MUTATED                                              2
  17Q LOSS WILD-TYPE                                           11
D69V4, multiclass
                                                                     clus
vv                                                                    17Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                8
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       2
                                                                     clus
vv                                                                    17Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 16
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     12
  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
  17Q LOSS MUTATED       0                         3    14
  17Q LOSS WILD-TYPE     3                         6    29
D69V5, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                3                  6
  WHITE                                   14                 29
[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(70) Variable = 18P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    7 10
  18P LOSS WILD-TYPE 14 24
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                17                 38 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                 24 
$`18P LOSS MUTATED`
TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N7-A4Y5 TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q3 
       18.08         4.87         0.26        26.70        18.81        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A5I1 TCGA-ND-A4W6 
       35.80        19.86       140.35        27.55        88.11        10.42 
TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
       23.47         9.80         5.49        14.53        12.43 

$`18P LOSS 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-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RO 
       25.18        19.30        52.31         4.67        59.38        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-A59B TCGA-N8-A4PI 
       19.63        17.16        51.75        25.35        27.19        26.63 
TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q8 
       13.74        25.68        12.20        21.93        67.17        15.81 
TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4WX 
       80.78         3.75        17.79         6.67         5.49        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VW 
        2.66        31.20 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.26               2.66 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            140.35              81.70 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            18.810             22.225 
[1] "0.3 - 140.3 (18.8)" "2.7 - 81.7 (22.2)" 
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   12  5
  18P LOSS WILD-TYPE 17 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     12    5
  18P LOSS WILD-TYPE   17   19
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                12                 17
  YES                5                 19
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  18P LOSS MUTATED                                                                    10
  18P LOSS WILD-TYPE                                                                  14
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  18P LOSS MUTATED                                                 7
  18P LOSS WILD-TYPE                                              12
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  18P LOSS MUTATED                                              1
  18P LOSS WILD-TYPE                                           12
D70V4, multiclass
                                                                     clus
vv                                                                    18P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               10
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       1
                                                                     clus
vv                                                                    18P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 14
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     12
  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
  18P LOSS MUTATED       2                         4    12
  18P LOSS WILD-TYPE     1                         5    31
D70V5, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                4                  5
  WHITE                                   12                 31
[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(71) Variable = 18Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    8 11
  18Q LOSS WILD-TYPE 13 23
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                19                 36 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                 23 
$`18Q LOSS MUTATED`
TCGA-N5-A4RN TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N6-A4V9 TCGA-N7-A4Y5 TCGA-N8-A4PN 
       34.62        18.08        22.52        32.19         0.26        26.70 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QX 
       67.17        54.97        35.80        19.86       140.35        27.55 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VU 
       88.11        10.42        23.47         9.80         5.49        14.53 
TCGA-N7-A4Y8 
       12.43 

$`18Q LOSS WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4WC 
       81.70         3.68         9.57        27.25        20.09        25.18 
TCGA-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RS 
       19.30        52.31         4.67        59.38         4.87        29.95 
TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VF 
       50.17        67.13        14.70        11.87        19.63        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PO 
       51.75        25.35        27.19        26.63        13.74        25.68 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QY 
       18.81        12.20        21.93        15.81        80.78         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VW 
       17.79         6.67         5.49        14.86         2.66        31.20 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.26               2.66 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            140.35              81.70 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            23.470             19.465 
[1] "0.3 - 140.3 (23.5)" "2.7 - 81.7 (19.5)" 
[1] "hr=" "1.5"
D71V2, continuous
D71V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   11  8
  18Q LOSS WILD-TYPE 18 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     11    8
  18Q LOSS WILD-TYPE   18   16
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                11                 18
  YES                8                 16
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  18Q LOSS MUTATED                                                                    12
  18Q LOSS WILD-TYPE                                                                  12
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  18Q LOSS MUTATED                                                 5
  18Q LOSS WILD-TYPE                                              14
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  18Q LOSS MUTATED                                              3
  18Q LOSS WILD-TYPE                                           10
D71V4, multiclass
                                                                     clus
vv                                                                    18Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               12
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       3
                                                                     clus
vv                                                                    18Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 12
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     14
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        10
[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
  18Q LOSS MUTATED       2                         6    12
  18Q LOSS WILD-TYPE     1                         3    31
D71V5, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                6                  3
  WHITE                                   12                 31
[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(72) Variable = 19P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    5 10
  19P LOSS WILD-TYPE 16 24
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                15                 40 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                10                 24 
$`19P LOSS MUTATED`
TCGA-N5-A4RT TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
       81.70        52.31         4.67        59.38        18.08         4.87 
TCGA-N5-A4RS TCGA-N6-A4V9 TCGA-N8-A4PL TCGA-N8-A56S TCGA-N9-A4Q7 TCGA-NA-A4R1 
       29.95        32.19        13.74        12.20        19.86         6.67 
TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-NF-A4WU 
       88.11        23.47         9.80 

$`19P LOSS 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-A4RO TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
       19.30        22.52        50.17        67.13        14.70        11.87 
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-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 
       26.63        26.70        25.68        18.81        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       54.97        35.80        15.81       140.35        80.78        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 
        3.75        17.79        10.42         5.49        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
        5.49        14.53        31.20        12.43 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              4.67               0.26 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             88.11             140.35 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             19.86              21.01 
[1] "4.7 - 88.1 (19.9)"  "0.3 - 140.3 (21.0)"
[1] "hr=" "1"  
D72V2, continuous
D72V3, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    7  7
  19P LOSS WILD-TYPE 22 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7    7
  19P LOSS WILD-TYPE   22   17
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 7                 22
  YES                7                 17
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  19P LOSS MUTATED                                                                     6
  19P LOSS WILD-TYPE                                                                  18
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  19P LOSS MUTATED                                                 6
  19P LOSS WILD-TYPE                                              13
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  19P LOSS MUTATED                                              3
  19P LOSS WILD-TYPE                                           10
D72V4, multiclass
                                                                     clus
vv                                                                    19P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                6
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    6
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       3
                                                                     clus
vv                                                                    19P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 18
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     13
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                        10
[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
  19P LOSS MUTATED       1                         2    12
  19P LOSS WILD-TYPE     2                         7    31
D72V5, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                2                  7
  WHITE                                   12                 31
[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(73) Variable = 19Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    5  7
  19Q LOSS WILD-TYPE 16 27
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                 43 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                 27 
$`19Q LOSS MUTATED`
TCGA-N5-A4RT TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RS 
       81.70        52.31         4.67        59.38         4.87        29.95 
TCGA-N6-A4V9 TCGA-N7-A59B TCGA-N8-A56S TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4WU 
       32.19        27.19        12.20         6.67         5.49         9.80 

$`19Q LOSS 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-A4RJ TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       19.30        18.08        22.52        50.17        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       11.87        19.63        17.16        51.75        25.35         0.26 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ 
       26.63        13.74        26.70        25.68        18.81        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-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
       23.47        14.86         2.66         5.49        14.53        31.20 
TCGA-N7-A4Y8 
       12.43 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              4.67               0.26 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             81.70             140.35 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            19.695             20.090 
[1] "4.7 - 81.7 (19.7)"  "0.3 - 140.3 (20.1)"
[1] "hr=" "1"  
D73V2, continuous
D73V3, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    4  6
  19Q LOSS WILD-TYPE 25 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    6
  19Q LOSS WILD-TYPE   25   18
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 4                 25
  YES                6                 18
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  19Q LOSS MUTATED                                                                     3
  19Q LOSS WILD-TYPE                                                                  21
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  19Q LOSS MUTATED                                                 5
  19Q LOSS WILD-TYPE                                              14
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  19Q LOSS MUTATED                                              4
  19Q LOSS WILD-TYPE                                            9
D73V4, multiclass
                                                                     clus
vv                                                                    19Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    5
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       4
                                                                     clus
vv                                                                    19Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 21
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     14
  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
  19Q LOSS MUTATED       0                         1    11
  19Q LOSS WILD-TYPE     3                         8    32
D73V5, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  8
  WHITE                                   11                 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"

Clustering(74) Variable = 20P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    4  4
  20P LOSS WILD-TYPE 17 30
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                 47 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 30 
$`20P LOSS MUTATED`
TCGA-N8-A4PP TCGA-N5-A4RJ TCGA-N6-A4VG TCGA-N7-A59B TCGA-N8-A56S TCGA-NA-A4QW 
       20.09        18.08        51.75        27.19        12.20        80.78 
TCGA-NA-A4R0 TCGA-NF-A4WU 
       17.79         9.80 

$`20P LOSS WILD-TYPE`
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-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO 
       19.30        52.31         4.67        59.38         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-N8-A4PI TCGA-N8-A4PL 
       19.63        17.16        25.35         0.26        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       26.70        25.68        18.81        21.93        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY 
       35.80        19.86        15.81       140.35        27.55         3.75 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX 
        6.67        88.11        10.42        23.47         5.49        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-N7-A4Y8 
        2.66         5.49        14.53        31.20        12.43 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              9.80               0.26 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             80.78             140.35 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            19.085             21.930 
[1] "9.8 - 80.8 (19.1)"  "0.3 - 140.3 (21.9)"
[1] "hr=" "1.3"
D74V2, continuous
D74V3, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    5  2
  20P LOSS WILD-TYPE 24 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5    2
  20P LOSS WILD-TYPE   24   22
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 5                 24
  YES                2                 22
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  20P LOSS MUTATED                                                                     3
  20P LOSS WILD-TYPE                                                                  21
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  20P LOSS MUTATED                                                 3
  20P LOSS WILD-TYPE                                              16
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  20P LOSS MUTATED                                              2
  20P LOSS WILD-TYPE                                           11
D74V4, multiclass
                                                                     clus
vv                                                                    20P LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                3
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    3
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       2
                                                                     clus
vv                                                                    20P LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 21
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     16
  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
  20P LOSS MUTATED       0                         0     8
  20P LOSS WILD-TYPE     3                         9    35
D74V5, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  9
  WHITE                                    8                 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(75) Variable = 20Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    3  2
  20Q LOSS WILD-TYPE 18 32
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                 50 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 32 
$`20Q LOSS MUTATED`
TCGA-N8-A4PP TCGA-N7-A59B TCGA-N8-A56S TCGA-NA-A4QW TCGA-NF-A4WU 
       20.09        27.19        12.20        80.78         9.80 

$`20Q LOSS WILD-TYPE`
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-QM-A5NM TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
       19.30        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-A4Y0 TCGA-N7-A4Y5 
       32.19        19.63        17.16        51.75        25.35         0.26 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ 
       26.63        13.74        26.70        25.68        18.81        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-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.55         3.75        17.79         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       23.47         5.49        14.86         2.66         5.49        14.53 
TCGA-NG-A4VW TCGA-N7-A4Y8 
       31.20        12.43 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              9.80               0.26 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             80.78             140.35 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            20.090             20.895 
[1] "9.8 - 80.8 (20.1)"  "0.3 - 140.3 (20.9)"
[1] "hr=" "1.6"
D75V2, continuous
D75V3, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  1
  20Q LOSS WILD-TYPE 26 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    1
  20Q LOSS WILD-TYPE   26   23
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 3                 26
  YES                1                 23
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  20Q LOSS MUTATED                                                                     2
  20Q LOSS WILD-TYPE                                                                  22
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  20Q LOSS MUTATED                                                 1
  20Q LOSS WILD-TYPE                                              18
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  20Q LOSS MUTATED                                              2
  20Q LOSS WILD-TYPE                                           11
D75V4, multiclass
                                                                     clus
vv                                                                    20Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                2
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    1
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       2
                                                                     clus
vv                                                                    20Q LOSS 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
  20Q LOSS MUTATED       0                         0     5
  20Q LOSS WILD-TYPE     3                         9    38
D75V5, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  9
  WHITE                                    5                 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"

Clustering(76) Variable = 21Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    5 12
  21Q LOSS WILD-TYPE 16 22
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                17                 38 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                12                 22 
$`21Q LOSS MUTATED`
TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N5-A4RA TCGA-N5-A4RU TCGA-N5-A59E TCGA-N6-A4VC 
       27.25        20.09        52.31        50.17        14.70        19.63 
TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A56S TCGA-N9-A4Q4 TCGA-N9-A4Q7 
        0.26        27.19        13.74        12.20        35.80        19.86 
TCGA-ND-A4WA TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU TCGA-N7-A4Y8 
       23.47        14.86         5.49        14.53        12.43 

$`21Q LOSS WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-ND-A4WC TCGA-QM-A5NM 
       34.62        81.70         3.68         9.57        25.18        19.30 
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS 
        4.67        59.38        18.08         4.87        22.52        29.95 
TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       67.13        11.87        32.19        17.16        51.75        25.35 
TCGA-N8-A4PI TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 
       26.63        26.70        25.68        18.81        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY 
       54.97        15.81       140.35        80.78        27.55         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WU 
       17.79         6.67        88.11        10.42         5.49         9.80 
TCGA-NF-A4X2 TCGA-NG-A4VW 
        2.66        31.20 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.26               2.66 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             52.31             140.35 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             19.63              23.85 
[1] "0.3 - 52.3 (19.6)"  "2.7 - 140.3 (23.9)"
[1] "hr=" "1.6"
D76V2, continuous
D76V3, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   14  1
  21Q LOSS WILD-TYPE 15 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     14    1
  21Q LOSS WILD-TYPE   15   23
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                14                 15
  YES                1                 23
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  21Q LOSS MUTATED                                                                     6
  21Q LOSS WILD-TYPE                                                                  18
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  21Q LOSS MUTATED                                                 7
  21Q LOSS WILD-TYPE                                              12
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  21Q LOSS MUTATED                                              4
  21Q LOSS WILD-TYPE                                            9
D76V4, multiclass
                                                                     clus
vv                                                                    21Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                6
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    7
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       4
                                                                     clus
vv                                                                    21Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 18
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                     12
  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
  21Q LOSS MUTATED       1                         2    13
  21Q LOSS WILD-TYPE     2                         7    30
D76V5, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                2                  7
  WHITE                                   13                 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(77) Variable = 22Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   10 23
  22Q LOSS WILD-TYPE 11 11
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                33                 22 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                23                 11 
$`22Q LOSS MUTATED`
TCGA-N5-A4RN TCGA-N6-A4VE TCGA-N8-A4PM TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RA 
       34.62         9.57        27.25        20.09        19.30        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-N7-A4Y5 TCGA-N8-A4PI 
       11.87        32.19        19.63        17.16         0.26        26.63 
TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       13.74        25.68        12.20        67.17        35.80        19.86 
TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
      140.35        27.55         3.75        17.79         6.67        88.11 
TCGA-ND-A4WA TCGA-NF-A4X2 TCGA-N7-A4Y8 
       23.47         2.66        12.43 

$`22Q LOSS WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-ND-A4WC TCGA-N5-A4RF TCGA-N5-A4RU TCGA-N5-A59E 
       81.70         3.68        25.18        59.38        50.17        14.70 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4PZ 
       51.75        25.35        27.19        26.70        18.81        21.93 
TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WU 
       54.97        15.81        80.78        10.42         5.49         9.80 
TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
       14.86         5.49        14.53        31.20 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.26               3.68 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            140.35              81.70 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            19.860             23.555 
[1] "0.3 - 140.3 (19.9)" "3.7 - 81.7 (23.6)" 
[1] "hr=" "1.5"
D77V2, continuous
D77V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   19 12
  22Q LOSS WILD-TYPE 10 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     19   12
  22Q LOSS WILD-TYPE   10   12
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                19                 10
  YES               12                 12
[1] 2 2
[1] FALSE
                    vv
clus                 UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  22Q LOSS MUTATED                                                                    13
  22Q LOSS WILD-TYPE                                                                  11
                    vv
clus                 UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  22Q LOSS MUTATED                                                13
  22Q LOSS WILD-TYPE                                               6
                    vv
clus                 UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  22Q LOSS MUTATED                                              7
  22Q LOSS WILD-TYPE                                            6
D77V4, multiclass
                                                                     clus
vv                                                                    22Q LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               13
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   13
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                       7
                                                                     clus
vv                                                                    22Q LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                 11
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                      6
  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
  22Q LOSS MUTATED       1                         8    24
  22Q LOSS WILD-TYPE     2                         1    19
D77V5, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                8                  1
  WHITE                                   24                 19
[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(78) Variable = XP LOSS MUTATION ANALYSIS
D78V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED    5 10
  XP LOSS WILD-TYPE 16 24
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               15                40 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               10                24 
$`XP LOSS MUTATED`
TCGA-N5-A4RN TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N6-A4V9 
       34.62        20.09        19.30        29.95        50.17        32.19 
TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-NA-A4QX 
        0.26        26.63        25.68        12.20        54.97        27.55 
TCGA-NA-A4R1 TCGA-ND-A4WA TCGA-ND-A4WF 
        6.67        23.47         5.49 

$`XP LOSS WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-ND-A4WC TCGA-N5-A4RA 
       81.70         3.68         9.57        27.25        25.18        52.31 
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RV 
        4.67        59.38        18.08         4.87        22.52        67.13 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       14.70        11.87        19.63        17.16        51.75        25.35 
TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 
       27.19        13.74        26.70        18.81        21.93        67.17 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY 
       35.80        19.86        15.81       140.35        80.78         3.75 
TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 
       17.79        88.11        10.42         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 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.26              2.66 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            54.97            140.35 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            25.68             19.22 
[1] "0.3 - 55.0 (25.7)"  "2.7 - 140.3 (19.2)"
[1] "hr=" "1.1"
D78V2, continuous
D78V3, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    8  7
  XP LOSS WILD-TYPE 21 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      8    7
  XP LOSS WILD-TYPE   21   17
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                8                21
  YES               7                17
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  XP LOSS MUTATED                                                                     5
  XP LOSS WILD-TYPE                                                                  19
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  XP LOSS MUTATED                                                 6
  XP LOSS WILD-TYPE                                              13
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  XP LOSS MUTATED                                              4
  XP LOSS WILD-TYPE                                            9
D78V4, multiclass
                                                                     clus
vv                                                                    XP LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               5
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   6
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      4
                                                                     clus
vv                                                                    XP LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                19
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    13
  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
  XP LOSS MUTATED       1                         2    12
  XP LOSS WILD-TYPE     2                         7    31
D78V5, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               2                 7
  WHITE                                  12                31
[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(79) Variable = XQ LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    6 12
  XQ LOSS WILD-TYPE 15 22
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18                37 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               12                22 
$`XQ LOSS MUTATED`
TCGA-N5-A4RN TCGA-N8-A4PP TCGA-QM-A5NM TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO 
       34.62        20.09        19.30        59.38         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N8-A4PI TCGA-N8-A56S 
       29.95        14.70        32.19        19.63        26.63        12.20 
TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4X2 
       54.97        15.81        27.55         6.67         5.49         2.66 

$`XQ LOSS WILD-TYPE`
TCGA-N5-A4RT TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N8-A4PM TCGA-ND-A4WC TCGA-N5-A4RA 
       81.70         3.68         9.57        27.25        25.18        52.31 
TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4VF 
        4.67        18.08        50.17        67.13        11.87        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN 
       51.75        25.35         0.26        27.19        13.74        26.70 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       25.68        18.81        21.93        67.17        35.80        19.86 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 
      140.35        80.78         3.75        17.79        88.11        10.42 
TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
       23.47         9.80        14.86         5.49        14.53        31.20 
TCGA-N7-A4Y8 
       12.43 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2.66              0.26 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            59.38            140.35 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            19.86             21.93 
[1] "2.7 - 59.4 (19.9)"  "0.3 - 140.3 (21.9)"
[1] "hr=" "1.3"
D79V2, continuous
D79V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    8 10
  XQ LOSS WILD-TYPE 21 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8   10
  XQ LOSS WILD-TYPE   21   14
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                8                21
  YES              10                14
[1] 2 2
[1] FALSE
                   vv
clus                UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS
  XQ LOSS MUTATED                                                                     7
  XQ LOSS WILD-TYPE                                                                  17
                   vv
clus                UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE
  XQ LOSS MUTATED                                                 6
  XQ LOSS WILD-TYPE                                              13
                   vv
clus                UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE
  XQ LOSS MUTATED                                              5
  XQ LOSS WILD-TYPE                                            8
D79V4, multiclass
                                                                     clus
vv                                                                    XQ LOSS MUTATED
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS               7
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                   6
  UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE                                      5
                                                                     clus
vv                                                                    XQ LOSS WILD-TYPE
  UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS                17
  UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE                                    13
  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
  XQ LOSS MUTATED       0                         2    16
  XQ LOSS WILD-TYPE     3                         7    27
D79V5, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               2                 7
  WHITE                                  16                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"
