[1] "ofn"        "-oTESCA-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/ESCA-TP/19775149/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/19782631/transformed.cor.cli.txt"

nPatients in clinical file=185, in cluster file=184, common to both=184
[1]  82 184
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               37               147 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               37               147 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               63               121 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               63               121 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               61               123 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               61               123 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               46               138 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               46               138 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               31               153 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               31               153 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               77               107 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               77               107 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               165 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               165 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18               166 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18               166 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               76               108 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               76               108 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               164 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               164 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38               146 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38               146 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               33               151 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               33               151 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              110                74 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              110                74 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               89                95 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               89                95 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               68               116 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               68               116 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              101                83 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              101                83 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               168 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               168 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               33               151 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               33               151 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                40                144 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                40                144 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                30                154 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                30                154 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                39                145 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                39                145 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                155 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                155 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                58                126 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                58                126 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                38                146 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                38                146 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                43                141 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                43                141 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                48                136 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                48                136 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                30                154 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                30                154 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                41                143 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                41                143 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                38                146 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                38                146 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                33                151 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                33                151 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                45                139 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                45                139 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                50                134 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                50                134 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                26                158 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                26                158 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                28                156 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                28                156 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                38                146 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                38                146 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               108                 76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               108                 76 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               115                 69 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               115                 69 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                18                166 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                18                166 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                153 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                153 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               23               161 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               23               161 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               38               146 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               38               146 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               38               146 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               38               146 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               162 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               162 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               173 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               173 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               166 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               166 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               93                91 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               93                91 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               33               151 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               33               151 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              105                79 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              105                79 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               87                97 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               87                97 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               46               138 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               46               138 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               86                98 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               86                98 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               39               145 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               39               145 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               39               145 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               39               145 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               171 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               171 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               22               162 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               22               162 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               63               121 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               63               121 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               23               161 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               23               161 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              101                83 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              101                83 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               65               119 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               65               119 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                50                134 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                50                134 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                135 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                135 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                52                132 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                52                132 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                58                126 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                58                126 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                151 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                151 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                153 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                153 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                67                117 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                67                117 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                139 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                139 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                57                127 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                57                127 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                54                130 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                54                130 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                131 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                131 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                71                113 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                71                113 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                159 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                159 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                71                113 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                71                113 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               102                 82 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               102                 82 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                65                119 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                65                119 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                52                132 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                52                132 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                165 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                165 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                176 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                176 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               106                 78 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               106                 78 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                72                112 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                72                112 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               60               124 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               60               124 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               40               144 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               40               144 
[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] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 184 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=74,	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=114,	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=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 184 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "HISTOLOGICAL_TYPE"           "NUMBER_PACK_YEARS_SMOKED"   
[11] "RESIDUAL_TUMOR"              "NUMBER_OF_LYMPH_NODES"      
[13] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
 1 31 43 87  5 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   32    43    87     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 31 43 87  5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   32    43    87     5 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
77 68 12  8 
[1] "table(vv)"
vv
N0 N1 N2 N3 
77 68 12  8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
77 68 12  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
77 68 12  8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=46, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=14, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED   20 17
  1P GAIN WILD-TYPE 87 59
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               37               146 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               17                59 
$`1P GAIN MUTATED`
TCGA-2H-A9GM TCGA-JY-A93E TCGA-L5-A4ON TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A891 
       13.94        25.22        18.35         7.43         0.36         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-R6-A6L4 
        3.02         2.66        13.22        13.41        10.36        16.31 
TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-VR-A8EQ TCGA-X8-AAAR TCGA-ZR-A9CJ 
       38.40        15.78        12.69        22.82        18.21        19.73 
TCGA-IG-A3QL TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-L5-A4OM TCGA-L7-A56G 
       35.21        17.03        23.41         4.67        47.93        10.85 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49X TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A8I0 
        5.92        10.45        12.62        13.22        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-V5-A7RC TCGA-VR-A8EW TCGA-XP-A8T6 
        0.13        12.03        12.26         3.42         8.12        25.08 
TCGA-Z6-A8JE 
        2.10 

$`1P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        8.94        16.24         4.21        32.45         7.69         3.88 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       14.86       122.10        60.39        47.38        34.85        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M 
       23.18        31.56         3.16        30.25        18.28         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00        26.33         4.70        32.61        19.99        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NG 
       29.00         7.13        22.82         2.60        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       12.92        13.48        16.47         7.76         5.49         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW 
       27.12        83.24        52.57        46.09        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.99         7.59         5.06         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        9.30         2.89         2.30         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4D TCGA-IC-A6RF TCGA-IG-A3I8 
       16.44         9.27         8.98        46.19        15.68        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I 
        0.53         0.79        12.82         9.96        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK 
        0.30         4.31        15.48        25.12         7.40        13.55 
TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       21.37        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       11.54        12.33         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-Q9-A6FU 
       12.23        12.03        13.18        13.18        12.85         5.16 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
       20.38        15.35        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       18.31        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       11.24         9.17        15.91        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.13              0.30 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            47.93            122.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           12.690            13.165 
[1] "0.1 - 47.9 (12.7)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "1.5"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         1        1        0        0         8         9
  1P GAIN WILD-TYPE       7        4        6        1        39        22
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           2          2          2          2        0
  1P GAIN WILD-TYPE        23         12          7          5        5
                   vv
clus                STAGE IVA
  1P GAIN MUTATED           2
  1P GAIN WILD-TYPE         2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 1                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                8                39
  STAGE IIB                9                22
  STAGE III                2                23
  STAGE IIIA               2                12
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 0                 5
  STAGE IVA                2                 2
[1] 12  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                T0+T1 T2 T3 T4
  1P GAIN MUTATED       8 10 14  0
  1P GAIN WILD-TYPE    24 33 73  5
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1               8                24
  T2                 10                33
  T3                 14                73
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  1P GAIN MUTATED   14 14  2  2
  1P GAIN WILD-TYPE 63 54 10  6
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              14                63
  N1              14                54
  N2               2                10
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    24   2
  1P GAIN WILD-TYPE 111   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     24    2
  1P GAIN WILD-TYPE  111    7
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              24               111
  1               2                 7
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     4  33
  1P GAIN WILD-TYPE  23 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4   33
  1P GAIN WILD-TYPE   23  124
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               4                23
  MALE                33               124
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    22  10
  1P GAIN WILD-TYPE 102  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     22   10
  1P GAIN WILD-TYPE  102   32
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               22               102
  YES              10                32
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   18 19
  1P GAIN WILD-TYPE 70 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     18   19
  1P GAIN WILD-TYPE   70   77
                                   clus
vv                                  1P GAIN MUTATED 1P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  18                70
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              19                77
[1] 2 2
[1] FALSE
D1V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    27   0   0   2
  1P GAIN WILD-TYPE 110  12   2   5
D1V12, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              27               110
  R1               0                12
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED      11                         3    22
  1P GAIN WILD-TYPE    35                         2    92
D1V14, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                  11                35
  BLACK OR AFRICAN AMERICAN               3                 2
  WHITE                                  22                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    2 22
  1P GAIN WILD-TYPE  4 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   22
  1P GAIN WILD-TYPE    4   66
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              22                66
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   33 30
  1Q GAIN WILD-TYPE 74 46
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               63               120 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               30                46 
$`1Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH 
       13.94         8.94        31.56        25.22        26.33        32.61 
TCGA-L5-A4ON TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       18.35         7.43         0.36         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L7-A6VZ 
        2.66        12.92        13.22         5.49        13.41        10.36 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-VR-A8EQ TCGA-VR-AA4D 
       16.31        38.40        15.78        12.69        22.82        46.19 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 
       18.21        19.73        35.21         0.85        20.12        18.64 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-L5-A43H 
       17.03         0.79        23.41        12.82         4.67         0.30 
TCGA-L5-A4OM TCGA-L5-A88Z TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U 
       47.93         7.40        10.85         5.92        10.45        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        12.62        12.49        12.76        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.33        12.00        13.18        13.38         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-V5-A7RC TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA7I 
       12.85        12.26         3.42         8.12        28.11        15.91 
TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08         2.10         1.32 

$`1Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
       16.24         4.21        32.45         7.69         3.88        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39        47.38        34.85        21.70        23.18 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
        3.16        30.25        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       19.99        21.01         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88V 
       58.59         4.90        29.00         7.13        22.82         2.60 
TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NT 
       35.97        13.48        16.47         7.76         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       83.24        52.57        46.09        33.11         7.82         7.99 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         5.06         7.04         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         2.30         7.00        20.02         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB 
        9.27         8.98        15.68        33.27        20.78         2.63 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.30         0.53         9.96        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J 
       68.02         3.68        41.52        24.03         6.28         4.31 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49N 
       15.48        25.12        13.55        21.37        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y 
       13.41        12.33        13.38        13.15        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I1 
       12.33        25.25        10.52        12.23        12.03        13.18 
TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
        5.16        20.38        15.35        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        1.55        18.31        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       11.24         9.17        41.23        14.37         3.42         2.66 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.13              0.53 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             55.5             122.1 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           12.820            13.315 
[1] "0.1 - 55.5 (12.8)"  "0.5 - 122.1 (13.3)"
[1] "hr=" "1.6"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         2        1        1        0        15        13
  1Q GAIN WILD-TYPE       6        4        5        1        32        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           7          5          3          3        2
  1Q GAIN WILD-TYPE        18          9          6          4        3
                   vv
clus                STAGE IVA
  1Q GAIN MUTATED           3
  1Q GAIN WILD-TYPE         1
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 1                 4
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA               15                32
  STAGE IIB               13                18
  STAGE III                7                18
  STAGE IIIA               5                 9
  STAGE IIIB               3                 6
  STAGE IIIC               3                 4
  STAGE IV                 2                 3
  STAGE IVA                3                 1
[1] 12  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                T0+T1 T2 T3 T4
  1Q GAIN MUTATED      14 15 27  2
  1Q GAIN WILD-TYPE    18 28 60  3
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              14                18
  T2                 15                28
  T3                 27                60
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  1Q GAIN MUTATED   25 27  3  3
  1Q GAIN WILD-TYPE 52 41  9  5
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              25                52
  N1              27                41
  N2               3                 9
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   46  5
  1Q GAIN WILD-TYPE 89  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     46    5
  1Q GAIN WILD-TYPE   89    4
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              46                89
  1               5                 4
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    5 58
  1Q GAIN WILD-TYPE 22 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   58
  1Q GAIN WILD-TYPE   22   99
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               5                22
  MALE                58                99
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   39 17
  1Q GAIN WILD-TYPE 85 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     39   17
  1Q GAIN WILD-TYPE   85   25
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               39                85
  YES              17                25
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   26 37
  1Q GAIN WILD-TYPE 62 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     26   37
  1Q GAIN WILD-TYPE   62   59
                                   clus
vv                                  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  26                62
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              37                59
[1] 2 2
[1] FALSE
D2V11, continuous
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   48  1  2  2
  1Q GAIN WILD-TYPE 89 11  0  5
D2V12, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              48                89
  R1               1                11
  R2               2                 0
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED      20                         3    37
  1Q GAIN WILD-TYPE    26                         2    77
D2V14, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                  20                26
  BLACK OR AFRICAN AMERICAN               3                 2
  WHITE                                  37                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2 36
  1Q GAIN WILD-TYPE  4 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   36
  1Q GAIN WILD-TYPE    4   52
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              36                52
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   32 28
  2P GAIN WILD-TYPE 75 48
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               60               123 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               28                48 
$`2P GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON 
       13.94         8.94        25.22        26.33        32.61        18.35 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NV 
        3.32         3.16         7.13         2.60         0.36        52.57 
TCGA-L7-A6VZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       10.36         7.99         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-A7RE TCGA-VR-AA4D 
       38.40         6.35        53.95        12.69        16.44        46.19 
TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6FA 
       18.21        15.68        18.64        23.41         4.67        44.75 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49R 
        4.31        47.93        10.85         5.92        10.45        13.38 
TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.15        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8I1 
       12.85        12.33        12.33        25.25        12.00        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP 
       12.85        12.26        20.38         3.42        15.35        27.09 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA7B TCGA-XP-A8T6 
       18.31         8.12        28.11        33.70        11.24        25.08 

$`2P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
       16.24         4.21        32.45         7.69         3.88        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       31.56         3.16        30.25        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        4.70        19.99        21.01         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A891 TCGA-L5-A893 
        4.90        29.00         7.43        22.82         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76         5.49         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-R6-A8W5 
       83.24        46.09        33.11         7.82         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW 
        2.89         2.30         7.00        20.02         5.29         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.98        22.82        19.73        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63        20.12         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
        0.79        12.82         9.96        14.50        12.16        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A88S 
        3.68        41.52        24.03         6.28         0.30        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49N 
       25.12         7.40        13.55        21.37        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        12.33        15.35        12.59        13.25        12.62 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       22.39        15.52        11.54        13.22         4.47        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        12.03        13.18        13.38         0.13        12.03 
TCGA-Q9-A6FU TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EZ TCGA-VR-A8Q7 
        5.16        25.81        12.43         1.55        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05         9.17        15.91        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        2.10         1.32         2.66 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.36              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            53.95            122.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           12.805            13.220 
[1] "0.4 - 54.0 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         1        3        2        1        13        13
  2P GAIN WILD-TYPE       7        2        4        0        34        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           6          1          3          2        2
  2P GAIN WILD-TYPE        19         13          6          5        3
                   vv
clus                STAGE IVA
  2P GAIN MUTATED           1
  2P GAIN WILD-TYPE         3
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 3                 2
  STAGE IB                 2                 4
  STAGE II                 1                 0
  STAGE IIA               13                34
  STAGE IIB               13                18
  STAGE III                6                19
  STAGE IIIA               1                13
  STAGE IIIB               3                 6
  STAGE IIIC               2                 5
  STAGE IV                 2                 3
  STAGE IVA                1                 3
[1] 12  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                T0+T1 T2 T3 T4
  2P GAIN MUTATED      13 13 24  0
  2P GAIN WILD-TYPE    19 30 63  5
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              13                19
  T2                 13                30
  T3                 24                63
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  2P GAIN MUTATED   24 20  3  3
  2P GAIN WILD-TYPE 53 48  9  5
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              24                53
  N1              20                48
  N2               3                 9
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   36  3
  2P GAIN WILD-TYPE 99  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     36    3
  2P GAIN WILD-TYPE   99    6
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              36                99
  1               3                 6
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     8  53
  2P GAIN WILD-TYPE  19 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8   53
  2P GAIN WILD-TYPE   19  104
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               8                19
  MALE                53               104
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   37 17
  2P GAIN WILD-TYPE 87 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     37   17
  2P GAIN WILD-TYPE   87   25
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               37                87
  YES              17                25
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   25 36
  2P GAIN WILD-TYPE 63 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     25   36
  2P GAIN WILD-TYPE   63   60
                                   clus
vv                                  2P GAIN MUTATED 2P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  25                63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              36                60
[1] 2 2
[1] FALSE
D3V11, continuous
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED   44  0  0  1
  2P GAIN WILD-TYPE 93 12  2  6
D3V12, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              44                93
  R1               0                12
  R2               0                 2
  RX               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED      21                         4    32
  2P GAIN WILD-TYPE    25                         1    82
D3V14, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                  21                25
  BLACK OR AFRICAN AMERICAN               4                 1
  WHITE                                  32                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    2 37
  2P GAIN WILD-TYPE  4 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   37
  2P GAIN WILD-TYPE    4   51
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              37                51
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   25 20
  2Q GAIN WILD-TYPE 82 56
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               45               138 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               20                56 
$`2Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO 
       13.94         8.94        25.22        26.33        32.61         3.32 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NV TCGA-Q9-A6FW 
        7.13         2.60         0.36        55.50        52.57         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.99         7.59         5.06        16.31        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-A7RE TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IC-A6RF 
       53.95        12.69        16.44        46.19        18.21        15.68 
TCGA-IG-A5S3 TCGA-JY-A6FA TCGA-L5-A43J TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A4A1 
       23.41        44.75         4.31         5.92        13.38        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.49        12.59        12.85        12.33        25.25        12.00 
TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EU 
       13.18        12.85        12.26         3.42        27.09        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-XP-A8T6 
        8.12        28.11        25.08 

$`2Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
       16.24         4.21        32.45         7.69         3.88        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       31.56         3.16        30.25        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        4.70        19.99        21.01        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T 
        3.16        58.59         4.90        29.00         7.43        22.82 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6L6 
       27.12        83.24        46.09        10.36        33.11         7.04 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         2.89         2.30         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-IG-A3I8 
        5.29         9.27         8.98        22.82        19.73        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        12.16        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
       24.03         6.28         0.30        47.93        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
        7.40        13.55        21.37        10.85        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 
       13.25        12.62        12.46        12.76        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       11.54        12.33        13.22         4.47        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FU 
       12.03        13.18        13.38         0.13        12.03         5.16 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EY 
       20.38        15.35        25.81        12.43         1.55        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.36              0.13 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             55.5             122.1 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           12.850            13.165 
[1] "0.4 - 55.5 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         1        1        1        1         9        11
  2Q GAIN WILD-TYPE       7        4        5        0        38        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           4          1          3          1        1
  2Q GAIN WILD-TYPE        21         13          6          6        4
                   vv
clus                STAGE IVA
  2Q GAIN MUTATED           1
  2Q GAIN WILD-TYPE         3
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 1                 4
  STAGE IB                 1                 5
  STAGE II                 1                 0
  STAGE IIA                9                38
  STAGE IIB               11                20
  STAGE III                4                21
  STAGE IIIA               1                13
  STAGE IIIB               3                 6
  STAGE IIIC               1                 6
  STAGE IV                 1                 4
  STAGE IVA                1                 3
[1] 12  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                T0+T1 T2 T3 T4
  2Q GAIN MUTATED      10 11 16  0
  2Q GAIN WILD-TYPE    22 32 71  5
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              10                22
  T2                 11                32
  T3                 16                71
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  2Q GAIN MUTATED   16 17  3  1
  2Q GAIN WILD-TYPE 61 51  9  7
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              16                61
  N1              17                51
  N2               3                 9
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    30   2
  2Q GAIN WILD-TYPE 105   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     30    2
  2Q GAIN WILD-TYPE  105    7
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              30               105
  1               2                 7
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     5  41
  2Q GAIN WILD-TYPE  22 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   41
  2Q GAIN WILD-TYPE   22  116
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               5                22
  MALE                41               116
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   31 10
  2Q GAIN WILD-TYPE 93 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     31   10
  2Q GAIN WILD-TYPE   93   32
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               31                93
  YES              10                32
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   23 23
  2Q GAIN WILD-TYPE 65 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     23   23
  2Q GAIN WILD-TYPE   65   73
                                   clus
vv                                  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  23                65
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              23                73
[1] 2 2
[1] FALSE
D4V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    30   0   0   2
  2Q GAIN WILD-TYPE 107  12   2   5
D4V12, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              30               107
  R1               0                12
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED      15                         2    25
  2Q GAIN WILD-TYPE    31                         3    89
D4V14, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                  15                31
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  25                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2 26
  2Q GAIN WILD-TYPE  4 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   26
  2Q GAIN WILD-TYPE    4   62
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              26                62
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   14 17
  3P GAIN WILD-TYPE 93 59
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               31               152 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17                59 
$`3P GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IC-A6RE TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A4OR 
       31.27        16.24         7.69        23.18        25.22         3.16 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-R6-A6KZ 
        3.75        55.50        27.12        52.57        10.36         5.06 
TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-AASW TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-IG-A4P3 
       53.95        12.69         9.27        22.82        19.73        18.64 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49R 
        0.30         4.31        47.93        10.85        10.45        13.38 
TCGA-LN-A4A1 TCGA-Q9-A6FU TCGA-VR-A8ER TCGA-VR-A8EX TCGA-VR-AA7B TCGA-XP-A8T8 
       12.59         5.16        12.43        28.11        11.24        14.37 
TCGA-Z6-A9VB 
        1.32 

$`3P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 
        8.94         4.21        32.45         3.88        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-L5-A43C 
       60.39        47.38        34.85        21.70        31.56         3.16 
TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25        18.28         8.94        24.00        26.33         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
       22.82         2.60         0.36         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW 
        8.71        13.41        83.24        46.09        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.99         7.59        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         2.89         2.30         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IC-A6RF 
        5.29        16.44         8.98        46.19        18.21        15.68 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A88S TCGA-L5-A88W 
        3.68        41.52        24.03         6.28        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
        7.40        13.55        21.37         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
       12.26        20.38         3.42        15.35        25.81        27.09 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
       18.05         9.17        15.91        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN 
        2.10         2.66 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.30              0.13 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             55.5             122.1 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           12.690            13.165 
[1] "0.3 - 55.5 (12.7)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0        2        0        0         3         7
  3P GAIN WILD-TYPE       8        3        6        1        44        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           4          2          2          2        1
  3P GAIN WILD-TYPE        21         12          7          5        4
                   vv
clus                STAGE IVA
  3P GAIN MUTATED           2
  3P GAIN WILD-TYPE         2
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 2                 3
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                3                44
  STAGE IIB                7                24
  STAGE III                4                21
  STAGE IIIA               2                12
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 1                 4
  STAGE IVA                2                 2
[1] 12  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                T0+T1 T2 T3 T4
  3P GAIN MUTATED       6  3 16  1
  3P GAIN WILD-TYPE    26 40 71  4
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1               6                26
  T2                  3                40
  T3                 16                71
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3P GAIN MUTATED    7 14  2  3
  3P GAIN WILD-TYPE 70 54 10  5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               7                70
  N1              14                54
  N2               2                10
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    18   3
  3P GAIN WILD-TYPE 117   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     18    3
  3P GAIN WILD-TYPE  117    6
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              18               117
  1               3                 6
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3  28
  3P GAIN WILD-TYPE  24 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   28
  3P GAIN WILD-TYPE   24  129
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3                24
  MALE                28               129
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    19  10
  3P GAIN WILD-TYPE 105  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     19   10
  3P GAIN WILD-TYPE  105   32
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               19               105
  YES              10                32
[1] 2 2
[1] FALSE
D5V9, continuous
D5V10, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   17 14
  3P GAIN WILD-TYPE 71 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     17   14
  3P GAIN WILD-TYPE   71   82
                                   clus
vv                                  3P GAIN MUTATED 3P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  17                71
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              14                82
[1] 2 2
[1] FALSE
D5V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    19   4   0   2
  3P GAIN WILD-TYPE 118   8   2   5
D5V12, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              19               118
  R1               4                 8
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       4                         2    21
  3P GAIN WILD-TYPE    42                         3    93
D5V14, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   4                42
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  21                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    2 13
  3P GAIN WILD-TYPE  4 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   13
  3P GAIN WILD-TYPE    4   75
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              13                75
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   45 31
  3Q GAIN WILD-TYPE 62 45
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               76               107 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               31                45 
$`3Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A4QS 
       31.27        58.55         7.63        16.24         7.69         3.88 
TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88V 
       60.39        23.18        25.22         3.16         7.13         2.60 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL 
        3.75        55.50         2.66        35.97        16.47        13.22 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-R6-A6DN 
        8.71        13.41        27.12        52.57        10.36         7.99 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-AASW TCGA-VR-A8EQ 
        7.59         5.06        53.95        12.69         9.27        22.82 
TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 
       19.73        33.27        35.21         0.85         2.63        18.64 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A97H TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM 
        0.53        17.03        14.50         0.30         4.31        47.93 
TCGA-L5-A88S TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       15.48        10.85        10.45        12.43        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.15        12.59        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A8I1 
       22.39        15.52        11.54        12.33        10.52        13.18 
TCGA-LN-A9FQ TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8ER TCGA-VR-A8EU 
       12.85         5.16        20.38         3.42        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        33.70        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB 
        9.17        41.23        14.37         1.32 

$`3Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       32.45        14.86       122.10        47.38        34.85        21.70 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       31.56         3.16        30.25        18.28         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       26.33         4.70        32.61        19.99        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
        7.43        22.82         0.36         3.02        12.92        13.48 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW 
        7.76         5.49        83.24        46.09        33.11         7.82 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         2.30         7.00        20.02         5.29        16.44 
TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YC 
        8.98        46.19        18.21        15.68        20.78        20.12 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        9.30         0.79        23.41        12.82         9.96         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K 
        6.28        25.12         7.40        13.55        21.37         5.92 
TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.66        12.33        15.35        13.25        12.62        12.46 
TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.85        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        12.03        13.18        13.38         0.13        12.03 
TCGA-LN-A9FR TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EZ 
       12.26        15.35        25.81        27.09         1.55        18.18 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.91        25.08         3.42         2.10         2.66 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.30              0.13 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            60.39            122.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           12.805            13.220 
[1] "0.3 - 60.4 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         2        2        2        0        19        11
  3Q GAIN WILD-TYPE       6        3        4        1        28        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED          13          7          4          3        2
  3Q GAIN WILD-TYPE        12          7          5          4        3
                   vv
clus                STAGE IVA
  3Q GAIN MUTATED           3
  3Q GAIN WILD-TYPE         1
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA               19                28
  STAGE IIB               11                20
  STAGE III               13                12
  STAGE IIIA               7                 7
  STAGE IIIB               4                 5
  STAGE IIIC               3                 4
  STAGE IV                 2                 3
  STAGE IVA                3                 1
[1] 12  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                T0+T1 T2 T3 T4
  3Q GAIN MUTATED      11 15 41  2
  3Q GAIN WILD-TYPE    21 28 46  3
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              11                21
  T2                 15                28
  T3                 41                46
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3Q GAIN MUTATED   29 30  5  4
  3Q GAIN WILD-TYPE 48 38  7  4
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              29                48
  N1              30                38
  N2               5                 7
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   56  5
  3Q GAIN WILD-TYPE 79  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     56    5
  3Q GAIN WILD-TYPE   79    4
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              56                79
  1               5                 4
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   11 66
  3Q GAIN WILD-TYPE 16 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     11   66
  3Q GAIN WILD-TYPE   16   91
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              11                16
  MALE                66                91
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   47 23
  3Q GAIN WILD-TYPE 77 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     47   23
  3Q GAIN WILD-TYPE   77   19
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               47                77
  YES              23                19
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   31 46
  3Q GAIN WILD-TYPE 57 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     31   46
  3Q GAIN WILD-TYPE   57   50
                                   clus
vv                                  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  31                57
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              46                50
[1] 2 2
[1] FALSE
D6V11, continuous
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED   60  5  0  3
  3Q GAIN WILD-TYPE 77  7  2  4
D6V12, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              60                77
  R1               5                 7
  R2               0                 2
  RX               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED      22                         3    43
  3Q GAIN WILD-TYPE    24                         2    71
D6V14, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                  22                24
  BLACK OR AFRICAN AMERICAN               3                 2
  WHITE                                  43                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3 40
  3Q GAIN WILD-TYPE  3 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   40
  3Q GAIN WILD-TYPE    3   48
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              40                48
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   10  9
  4P GAIN WILD-TYPE 97 67
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               164 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9                67 
$`4P GAIN MUTATED`
TCGA-JY-A6F8 TCGA-L5-A43I TCGA-L5-A4ON TCGA-L5-A8NE TCGA-L5-A8NV TCGA-R6-A6XG 
      122.10        18.28        18.35        55.50        52.57        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-X8-AAAR TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-L5-A43J 
       53.95         9.30        18.21         2.63        23.41         4.31 
TCGA-L7-A56G TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HY TCGA-VR-A8EO TCGA-XP-A8T6 
       10.85        11.54         4.47        12.03        25.81        25.08 
TCGA-Z6-AAPN 
        2.66 

$`4P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
        3.88        14.86        60.39        47.38        34.85        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
       23.18        31.56        25.22         3.16        30.25         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00        26.33         4.70        32.61        19.99        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y 
       29.00         7.13         7.43        22.82         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       27.12        83.24        46.09        10.36        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.99         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         2.30        12.69         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
        5.29        16.44         9.27         8.98        22.82        46.19 
TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       19.73        15.68        33.27        35.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H 
       68.02         3.68        41.52        24.03         6.28         0.30 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ 
       47.93        15.48        25.12         7.40        13.55        21.37 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.85        15.52        12.33        13.22        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       10.52        12.00        12.23        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW 
        0.13        12.03        12.85        12.26         5.16        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        3.42        15.35        27.09        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       11.24         9.17        15.91        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB 
        2.10         1.32 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             2.63              0.13 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           122.10             83.24 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           18.280            12.885 
[1] "2.6 - 122.1 (18.3)" "0.1 - 83.2 (12.9)" 
[1] "hr=" "1.3"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         1        0        0        0         4         5
  4P GAIN WILD-TYPE       7        5        6        1        43        26
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           1          2          0          0        1
  4P GAIN WILD-TYPE        24         12          9          7        4
                   vv
clus                STAGE IVA
  4P GAIN MUTATED           0
  4P GAIN WILD-TYPE         4
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                4                43
  STAGE IIB                5                26
  STAGE III                1                24
  STAGE IIIA               2                12
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  4P GAIN MUTATED       3  3  9  0
  4P GAIN WILD-TYPE    29 40 78  5
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               3                29
  T2                  3                40
  T3                  9                78
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4P GAIN MUTATED    7  8  0  0
  4P GAIN WILD-TYPE 70 60 12  8
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               7                70
  N1               8                60
  N2               0                12
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    10   1
  4P GAIN WILD-TYPE 125   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     10    1
  4P GAIN WILD-TYPE  125    8
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              10               125
  1               1                 8
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  18
  4P GAIN WILD-TYPE  26 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   18
  4P GAIN WILD-TYPE   26  139
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                26
  MALE                18               139
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    13   4
  4P GAIN WILD-TYPE 111  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     13    4
  4P GAIN WILD-TYPE  111   38
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               13               111
  YES               4                38
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    9 10
  4P GAIN WILD-TYPE 79 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      9   10
  4P GAIN WILD-TYPE   79   86
                                   clus
vv                                  4P GAIN MUTATED 4P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   9                79
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              10                86
[1] 2 2
[1] FALSE
D7V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    10   1   1   1
  4P GAIN WILD-TYPE 127  11   1   6
D7V12, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              10               127
  R1               1                11
  R2               1                 1
  RX               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       3                         2    14
  4P GAIN WILD-TYPE    43                         3   100
D7V14, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   3                43
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  14               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2 10
  4P GAIN WILD-TYPE  4 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2   10
  4P GAIN WILD-TYPE    4   78
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              10                78
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   10  8
  4Q GAIN WILD-TYPE 97 68
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18               165 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8                68 
$`4Q GAIN MUTATED`
TCGA-JY-A6F8 TCGA-L5-A4ON TCGA-L5-A8NE TCGA-L5-A8NV TCGA-R6-A6Y0 TCGA-X8-AAAR 
      122.10        18.35        55.50        52.57        53.95        18.21 
TCGA-IG-A3YA TCGA-IG-A5S3 TCGA-L5-A43H TCGA-L7-A56G TCGA-LN-A4A8 TCGA-LN-A4A9 
       20.78        23.41         0.30        10.85        15.52        11.54 
TCGA-LN-A7HY TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EW TCGA-XP-A8T6 TCGA-Z6-AAPN 
       12.03         3.42        25.81         8.12        25.08         2.66 

$`4Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
        3.88        14.86        60.39        47.38        34.85        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I 
       23.18        31.56        25.22         3.16        30.25        18.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00        26.33         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        22.82         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         3.75         3.02         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       13.48        16.47        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       13.41        27.12        83.24        46.09        10.36        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         7.99         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.02         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 
        8.98        22.82        46.19        19.73        15.68        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       35.21         0.85         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.53        17.03         0.79        12.82         9.96         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
       24.03         6.28         4.31        47.93        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
        7.40        13.55        21.37         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.76        12.59        22.39        12.85        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER 
       12.26         5.16        20.38        15.35        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 
       18.05        11.24         9.17        15.91        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
        3.42         2.10         1.32 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.30              0.13 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           122.10             83.24 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            18.28             12.85 
[1] "0.3 - 122.1 (18.3)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.4"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         1        0        0        0         5         4
  4Q GAIN WILD-TYPE       7        5        6        1        42        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           2          1          1          0        0
  4Q GAIN WILD-TYPE        23         13          8          7        5
                   vv
clus                STAGE IVA
  4Q GAIN MUTATED           0
  4Q GAIN WILD-TYPE         4
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                5                42
  STAGE IIB                4                27
  STAGE III                2                23
  STAGE IIIA               1                13
  STAGE IIIB               1                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  4Q GAIN MUTATED       3  4  7  1
  4Q GAIN WILD-TYPE    29 39 80  4
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               3                29
  T2                  4                39
  T3                  7                80
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4Q GAIN MUTATED    8  6  1  0
  4Q GAIN WILD-TYPE 69 62 11  8
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               8                69
  N1               6                62
  N2               1                11
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    13   0
  4Q GAIN WILD-TYPE 122   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     13    0
  4Q GAIN WILD-TYPE  122    9
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              13               122
  1               0                 9
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  17
  4Q GAIN WILD-TYPE  26 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   17
  4Q GAIN WILD-TYPE   26  140
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                26
  MALE                17               140
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    14   3
  4Q GAIN WILD-TYPE 110  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     14    3
  4Q GAIN WILD-TYPE  110   39
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               14               110
  YES               3                39
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    6 12
  4Q GAIN WILD-TYPE 82 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6   12
  4Q GAIN WILD-TYPE   82   84
                                   clus
vv                                  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   6                82
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              12                84
[1] 2 2
[1] FALSE
D8V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    12   1   0   0
  4Q GAIN WILD-TYPE 125  11   2   7
D8V12, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              12               125
  R1               1                11
  R2               0                 2
  RX               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       4                         3    11
  4Q GAIN WILD-TYPE    42                         2   103
D8V14, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   4                42
  BLACK OR AFRICAN AMERICAN               3                 2
  WHITE                                  11               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    1 10
  4Q GAIN WILD-TYPE  5 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   10
  4Q GAIN WILD-TYPE    5   78
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              10                78
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   47 28
  5P GAIN WILD-TYPE 60 48
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               75               108 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               28                48 
$`5P GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
       14.30         5.92        32.45        47.38        31.56        25.22 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO TCGA-L5-A4OP 
       18.28         8.94        32.61        19.99         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NE 
        3.16         4.90        29.00         7.13         0.36        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-R6-A6KZ TCGA-R6-A6L4 
       35.97        12.92        52.57        10.36         5.06        16.31 
TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC 
       53.95         7.00        19.73        33.27         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD 
       18.64         0.79        23.41        14.50        44.75        68.02 
TCGA-JY-A6FE TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A8NK 
        3.68         0.30         4.31        47.93        15.48        13.55 
TCGA-L7-A56G TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       10.85        13.41        13.38        13.25        12.46        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.59        12.85        12.33        13.22         4.47        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.00        12.23        13.18        13.18        12.85        12.26 
TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EY 
        5.16        20.38         3.42        27.09        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 
       52.27        18.05        11.24        15.91        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
        3.42         2.10         1.32 

$`5P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 
       16.24         4.21         7.69         3.88        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E 
       60.39        34.85        21.70        23.18         3.16        30.25 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
       24.00        26.33         4.70        21.01        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
       58.59         7.43        22.82         2.60         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-M9-A5M8 
        8.71        13.41        27.12        83.24        46.09        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         7.99         7.59         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
        9.30        15.78         2.89         2.30        12.69        20.02 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
        5.29        16.44         9.27         8.98        22.82        46.19 
TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT 
       18.21        15.68        35.21         0.85        20.78         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I 
        0.53        17.03        12.82         9.96         4.67        12.16 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ 
       41.52        24.03         6.28        25.12         7.40        21.37 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S 
        5.92        10.45        12.66        12.43        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       15.35        12.59        12.62        12.49        12.76        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A8I0 
       15.52        11.54        25.25        10.52        12.03        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET 
        0.13        12.03        15.35        25.81        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-AAPN 
       18.31         8.12        18.18         9.17        41.23         2.66 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.30              0.13 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            68.02            122.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           13.220            12.725 
[1] "0.3 - 68.0 (13.2)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         1        3        3        1        18        13
  5P GAIN WILD-TYPE       7        2        3        0        29        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED          10          8          2          5        4
  5P GAIN WILD-TYPE        15          6          7          2        1
                   vv
clus                STAGE IVA
  5P GAIN MUTATED           1
  5P GAIN WILD-TYPE         3
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 3                 2
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               18                29
  STAGE IIB               13                18
  STAGE III               10                15
  STAGE IIIA               8                 6
  STAGE IIIB               2                 7
  STAGE IIIC               5                 2
  STAGE IV                 4                 1
  STAGE IVA                1                 3
[1] 12  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                T0+T1 T2 T3 T4
  5P GAIN MUTATED       9 18 43  1
  5P GAIN WILD-TYPE    23 25 44  4
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1               9                23
  T2                 18                25
  T3                 43                44
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5P GAIN MUTATED   31 29  4  6
  5P GAIN WILD-TYPE 46 39  8  2
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              31                46
  N1              29                39
  N2               4                 8
  N3               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   54  5
  5P GAIN WILD-TYPE 81  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     54    5
  5P GAIN WILD-TYPE   81    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              54                81
  1               5                 4
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   14 62
  5P GAIN WILD-TYPE 13 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     14   62
  5P GAIN WILD-TYPE   13   95
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              14                13
  MALE                62                95
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   53 16
  5P GAIN WILD-TYPE 71 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     53   16
  5P GAIN WILD-TYPE   71   26
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               53                71
  YES              16                26
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   27 49
  5P GAIN WILD-TYPE 61 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     27   49
  5P GAIN WILD-TYPE   61   47
                                   clus
vv                                  5P GAIN MUTATED 5P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  27                61
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              49                47
[1] 2 2
[1] FALSE
D9V11, continuous
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   55  7  2  4
  5P GAIN WILD-TYPE 82  5  0  3
D9V12, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              55                82
  R1               7                 5
  R2               2                 0
  RX               4                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED      21                         4    45
  5P GAIN WILD-TYPE    25                         1    69
D9V14, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                  21                25
  BLACK OR AFRICAN AMERICAN               4                 1
  WHITE                                  45                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2 37
  5P GAIN WILD-TYPE  4 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   37
  5P GAIN WILD-TYPE    4   51
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              37                51
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   14  5
  5Q GAIN WILD-TYPE 93 71
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               164 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5                71 
$`5Q GAIN MUTATED`
TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO TCGA-L7-A6VZ 
       25.22         8.94        32.61        19.99         3.32        10.36 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-RE-A7BO TCGA-IG-A3I8 TCGA-L5-A88S TCGA-LN-A49Y 
        5.06        16.31         7.00        33.27        15.48        12.46 
TCGA-LN-A4A1 TCGA-LN-A4MR TCGA-LN-A7HW TCGA-LN-A7HX TCGA-V5-A7RC TCGA-VR-AA7B 
       12.59        13.22        12.00        12.23         3.42        11.24 
TCGA-VR-AA7I 
       15.91 

$`5Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 
        3.88        14.86       122.10        60.39        47.38        34.85 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I 
       21.70        23.18        31.56         3.16        30.25        18.28 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP 
       24.00        26.33         4.70        21.01        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        7.43        22.82         2.60         0.36         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76         5.49         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       83.24        52.57        46.09        33.11         7.82         7.99 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89         2.30        12.69        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR 
       16.44         9.27         8.98        22.82        46.19        18.21 
TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       19.73        15.68        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK 
        0.30         4.31        47.93        25.12         7.40        13.55 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.25        12.62        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        15.52        11.54        12.33         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       25.25        10.52        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW 
        0.13        12.03        12.85        12.26         5.16        20.38 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35        25.81        27.09        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             3.32              0.13 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            33.27            122.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            12.46             13.18 
[1] "3.3 - 33.3 (12.5)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         1        0        1        0         7         1
  5Q GAIN WILD-TYPE       7        5        5        1        40        30
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           1          1          0          3        1
  5Q GAIN WILD-TYPE        24         13          9          4        4
                   vv
clus                STAGE IVA
  5Q GAIN MUTATED           0
  5Q GAIN WILD-TYPE         4
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                7                40
  STAGE IIB                1                30
  STAGE III                1                24
  STAGE IIIA               1                13
  STAGE IIIB               0                 9
  STAGE IIIC               3                 4
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  5Q GAIN MUTATED       2  4 10  1
  5Q GAIN WILD-TYPE    30 39 77  4
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               2                30
  T2                  4                39
  T3                 10                77
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5Q GAIN MUTATED   10  2  1  4
  5Q GAIN WILD-TYPE 67 66 11  4
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              10                67
  N1               2                66
  N2               1                11
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    12   1
  5Q GAIN WILD-TYPE 123   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     12    1
  5Q GAIN WILD-TYPE  123    8
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              12               123
  1               1                 8
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     4  16
  5Q GAIN WILD-TYPE  23 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4   16
  5Q GAIN WILD-TYPE   23  141
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               4                23
  MALE                16               141
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    16   3
  5Q GAIN WILD-TYPE 108  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     16    3
  5Q GAIN WILD-TYPE  108   39
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               16               108
  YES               3                39
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    9 11
  5Q GAIN WILD-TYPE 79 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      9   11
  5Q GAIN WILD-TYPE   79   85
                                   clus
vv                                  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   9                79
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              11                85
[1] 2 2
[1] FALSE
D10V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    13   1   1   1
  5Q GAIN WILD-TYPE 124  11   1   6
D10V12, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              13               124
  R1               1                11
  R2               1                 1
  RX               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       6                         1    12
  5Q GAIN WILD-TYPE    40                         4   102
D10V14, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   6                40
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  12               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    0 12
  5Q GAIN WILD-TYPE  6 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   12
  5Q GAIN WILD-TYPE    6   76
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              12                76
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   20 18
  6P GAIN WILD-TYPE 87 58
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38               145 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               18                58 
$`6P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63        13.94        16.24 
TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-L5-A43E TCGA-L5-A4OS TCGA-L5-A88V TCGA-L5-A891 
        3.88       122.10        30.25        58.59         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NT 
        3.02        55.50         2.66        12.92         5.49        27.12 
TCGA-L7-A6VZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-IG-A8O2 TCGA-IG-A97H 
       10.36        16.31         7.04        15.78         4.67        14.50 
TCGA-JY-A6FD TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49L 
       68.02        47.93        15.48        21.37        10.85        10.45 
TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 
       13.15        12.62        12.33        12.00        12.23        13.18 
TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.91         2.10 

$`6P GAIN WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       58.55         5.92         8.94         4.21        32.45         7.69 
TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       14.86        60.39        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       31.56        25.22         3.16        18.28         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       26.33         4.70        32.61        19.99        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NI 
        7.13         7.43        22.82         0.36        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       16.47        13.22         7.76         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       52.57        46.09        33.11         7.82         7.99         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
        5.06        38.40         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.02         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ 
        9.27         8.98        22.82        46.19        18.21        19.73 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       15.68        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE 
       23.41        12.82         9.96        12.16        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88W 
       41.52        24.03         6.28         0.30         4.31        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
        7.40        13.55         5.92        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
       12.33        13.38        15.35        12.59        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       10.52        12.03        13.18        13.38         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       12.85        12.26         5.16        20.38         3.42        15.35 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
        9.17        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN 
        2.66 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             2.10              0.13 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           122.10             83.24 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           13.165            12.850 
[1] "2.1 - 122.1 (13.2)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         3        1        1        0         9         5
  6P GAIN WILD-TYPE       5        4        5        1        38        26
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           7          1          2          1        1
  6P GAIN WILD-TYPE        18         13          7          6        4
                   vv
clus                STAGE IVA
  6P GAIN MUTATED           3
  6P GAIN WILD-TYPE         1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 1                 4
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                9                38
  STAGE IIB                5                26
  STAGE III                7                18
  STAGE IIIA               1                13
  STAGE IIIB               2                 7
  STAGE IIIC               1                 6
  STAGE IV                 1                 4
  STAGE IVA                3                 1
[1] 12  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                T0+T1 T2 T3 T4
  6P GAIN MUTATED       8  7 19  1
  6P GAIN WILD-TYPE    24 36 68  4
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1               8                24
  T2                  7                36
  T3                 19                68
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6P GAIN MUTATED   17 14  2  1
  6P GAIN WILD-TYPE 60 54 10  7
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              17                60
  N1              14                54
  N2               2                10
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    27   4
  6P GAIN WILD-TYPE 108   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     27    4
  6P GAIN WILD-TYPE  108    5
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              27               108
  1               4                 5
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5  33
  6P GAIN WILD-TYPE  22 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5   33
  6P GAIN WILD-TYPE   22  124
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5                22
  MALE                33               124
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   26  8
  6P GAIN WILD-TYPE 98 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     26    8
  6P GAIN WILD-TYPE   98   34
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               26                98
  YES               8                34
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   22 16
  6P GAIN WILD-TYPE 66 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     22   16
  6P GAIN WILD-TYPE   66   80
                                   clus
vv                                  6P GAIN MUTATED 6P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  22                66
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              16                80
[1] 2 2
[1] FALSE
D11V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    29   3   1   1
  6P GAIN WILD-TYPE 108   9   1   6
D11V12, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              29               108
  R1               3                 9
  R2               1                 1
  RX               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED      10                         1    21
  6P GAIN WILD-TYPE    36                         4    93
D11V14, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                  10                36
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  21                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    0 16
  6P GAIN WILD-TYPE  6 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   16
  6P GAIN WILD-TYPE    6   72
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              16                72
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   17 16
  6Q GAIN WILD-TYPE 90 60
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               33               150 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                60 
$`6Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS 
       31.27        14.30         7.63        13.94        16.24         3.88 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43E TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE 
      122.10        60.39        30.25         2.60         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        2.66        12.92        27.12        10.36        16.31         7.04 
TCGA-R6-A8W5 TCGA-IG-A97H TCGA-JY-A6FD TCGA-L5-A88S TCGA-L5-A8NQ TCGA-L7-A56G 
       15.78        14.50        68.02        15.48        21.37        10.85 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HX 
       10.45        13.15        12.62        12.33         4.47        12.23 
TCGA-LN-A8I1 TCGA-VR-AA7I TCGA-Z6-A8JE 
       13.18        15.91         2.10 

$`6Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78        58.55         5.92         8.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        7.69        14.86        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       31.56        25.22         3.16        18.28         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       26.33         4.70        32.61        19.99        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A891 
       29.00         7.13         7.43        22.82         0.36         3.75 
TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 
        8.71        13.41        83.24        52.57        46.09        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         7.99         7.59         5.06        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
       20.02         5.29        16.44         9.27         8.98        22.82 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       46.19        18.21        19.73        15.68        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
        4.67        12.16        44.75         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z 
        6.28         0.30         4.31        47.93        25.12         7.40 
TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       13.55         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       13.38        15.35        12.59        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       11.54        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.03        13.18        13.38         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO 
       12.26         5.16        20.38         3.42        15.35        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        18.05        11.24         9.17 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             2.10              0.13 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           122.10             83.24 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            13.18             12.85 
[1] "2.1 - 122.1 (13.2)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         4        0        1        0         8         4
  6Q GAIN WILD-TYPE       4        5        5        1        39        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           5          1          1          1        2
  6Q GAIN WILD-TYPE        20         13          8          6        3
                   vv
clus                STAGE IVA
  6Q GAIN MUTATED           3
  6Q GAIN WILD-TYPE         1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  4                 4
  STAGE IA                 0                 5
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                8                39
  STAGE IIB                4                27
  STAGE III                5                20
  STAGE IIIA               1                13
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 2                 3
  STAGE IVA                3                 1
[1] 12  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                T0+T1 T2 T3 T4
  6Q GAIN MUTATED       8  5 16  1
  6Q GAIN WILD-TYPE    24 38 71  4
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               8                24
  T2                  5                38
  T3                 16                71
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6Q GAIN MUTATED   16 11  1  1
  6Q GAIN WILD-TYPE 61 57 11  7
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              16                61
  N1              11                57
  N2               1                11
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    22   5
  6Q GAIN WILD-TYPE 113   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     22    5
  6Q GAIN WILD-TYPE  113    4
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              22               113
  1               5                 4
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3  30
  6Q GAIN WILD-TYPE  24 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   30
  6Q GAIN WILD-TYPE   24  127
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                24
  MALE                30               127
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    23   8
  6Q GAIN WILD-TYPE 101  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     23    8
  6Q GAIN WILD-TYPE  101   34
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               23               101
  YES               8                34
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   19 14
  6Q GAIN WILD-TYPE 69 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     19   14
  6Q GAIN WILD-TYPE   69   82
                                   clus
vv                                  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  19                69
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              14                82
[1] 2 2
[1] FALSE
D12V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    24   2   2   1
  6Q GAIN WILD-TYPE 113  10   0   6
D12V12, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              24               113
  R1               2                10
  R2               2                 0
  RX               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       9                         1    18
  6Q GAIN WILD-TYPE    37                         4    96
D12V14, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   9                37
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  18                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    0 15
  6Q GAIN WILD-TYPE  6 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   15
  6Q GAIN WILD-TYPE    6   73
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              15                73
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   67 42
  7P GAIN WILD-TYPE 40 34
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              109                74 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               42                34 
$`7P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78         5.92        13.94         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C 
        7.69        60.39        21.70        23.18        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4ON 
       30.25        24.00        26.33         4.70        32.61        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        3.32         1.38         3.16        58.59         4.90         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         0.36         3.75         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT 
       12.92        16.47        13.22         5.49         8.71        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       52.57        46.09        10.36         7.82         7.99         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASW 
        9.30         2.30        12.69         7.00         5.29         9.27 
TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IG-A3QL TCGA-IG-A3YB 
        8.98        46.19        18.21        19.73        35.21         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12        18.64         0.53        17.03         0.79        23.41 
TCGA-IG-A97H TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88S TCGA-L5-A8NK TCGA-L7-A56G 
       14.50         0.30         4.31        15.48        13.55        10.85 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
        5.92        12.43        13.41        13.38        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.85        12.33        13.22        12.33        25.25        12.00 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
        0.13        12.85        12.26        20.38         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       27.09         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       11.24        15.91        25.08        14.37         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

$`7P GAIN WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GQ TCGA-IG-A4QS 
       31.27        14.30        58.55         7.63         4.21         3.88 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43I 
       14.86       122.10        47.38        34.85        31.56        18.28 
TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A4OX 
        8.94        19.99        21.01         7.17        29.00         7.43 
TCGA-L5-A88T TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NS TCGA-L5-A8NU 
       22.82        55.50        13.48         7.76        13.41        83.24 
TCGA-M9-A5M8 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-A7RE TCGA-VR-A8EQ 
       33.11        15.78         2.89        20.02        16.44        22.82 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A625 
       15.68        33.27         0.85        20.78         9.30        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        9.96         4.67        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z 
       41.52        24.03         6.28        47.93        25.12         7.40 
TCGA-L5-A8NQ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49Y 
       21.37        10.45        12.66        12.33        13.15        12.46 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       22.39        15.52        11.54         4.47        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-Q9-A6FU 
       12.03        13.18        13.38        13.18        12.03         5.16 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
       25.81        12.43        18.18        52.27        18.05         9.17 
TCGA-XP-A8T7 TCGA-Z6-A8JD 
       41.23         3.42 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.13              0.85 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            60.39            122.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            12.62             13.89 
[1] "0.1 - 60.4 (12.6)"  "0.8 - 122.1 (13.9)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         5        1        4        1        21        20
  7P GAIN WILD-TYPE       3        4        2        0        26        11
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          16          7          5          3        4
  7P GAIN WILD-TYPE         9          7          4          4        1
                   vv
clus                STAGE IVA
  7P GAIN MUTATED           3
  7P GAIN WILD-TYPE         1
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  5                 3
  STAGE IA                 1                 4
  STAGE IB                 4                 2
  STAGE II                 1                 0
  STAGE IIA               21                26
  STAGE IIB               20                11
  STAGE III               16                 9
  STAGE IIIA               7                 7
  STAGE IIIB               5                 4
  STAGE IIIC               3                 4
  STAGE IV                 4                 1
  STAGE IVA                3                 1
[1] 12  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                T0+T1 T2 T3 T4
  7P GAIN MUTATED      22 18 53  1
  7P GAIN WILD-TYPE    10 25 34  4
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              22                10
  T2                 18                25
  T3                 53                34
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   38 45  6  4
  7P GAIN WILD-TYPE 39 23  6  4
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              38                39
  N1              45                23
  N2               6                 6
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   72  7
  7P GAIN WILD-TYPE 63  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     72    7
  7P GAIN WILD-TYPE   63    2
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              72                63
  1               7                 2
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   11 99
  7P GAIN WILD-TYPE 16 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     11   99
  7P GAIN WILD-TYPE   16   58
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              11                16
  MALE                99                58
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   74 22
  7P GAIN WILD-TYPE 50 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     74   22
  7P GAIN WILD-TYPE   50   20
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               74                50
  YES              22                20
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   58 52
  7P GAIN WILD-TYPE 30 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     58   52
  7P GAIN WILD-TYPE   30   44
                                   clus
vv                                  7P GAIN MUTATED 7P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  58                30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              52                44
[1] 2 2
[1] FALSE
D13V11, continuous
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   75  8  1  5
  7P GAIN WILD-TYPE 62  4  1  2
D13V12, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              75                62
  R1               8                 4
  R2               1                 1
  RX               5                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED      26                         5    69
  7P GAIN WILD-TYPE    20                         0    45
D13V14, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                  26                20
  BLACK OR AFRICAN AMERICAN               5                 0
  WHITE                                  69                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5 54
  7P GAIN WILD-TYPE  1 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5   54
  7P GAIN WILD-TYPE    1   34
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 1
  NOT HISPANIC OR LATINO              54                34
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   54 34
  7Q GAIN WILD-TYPE 53 42
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               88                95 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               34                42 
$`7Q GAIN MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-JY-A6FB TCGA-JY-A939 
        8.94        16.24        32.45         7.69        60.39        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OE 
       23.18        31.56        25.22         3.16        30.25        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT 
       26.33         4.70        32.61         3.32         3.16         4.90 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         0.36         3.75         3.02         2.66        35.97 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.22         5.49        27.12        52.57        46.09        10.36 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         7.99        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASW 
        9.30         2.30        12.69         7.00         5.29         9.27 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4P3 
       46.19        18.21        19.73        35.21        20.12        18.64 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A97H TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM 
       17.03        23.41        14.50         0.30         4.31        47.93 
TCGA-L5-A88S TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       15.48        10.85         5.92        13.41        12.33        13.38 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       15.35        12.59        13.25        12.49        12.76        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       12.00         0.13        12.85        20.38         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       27.09        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       11.24        25.08         2.10         1.32 

$`7Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH 
       13.94         4.21         3.88        14.86       122.10        47.38 
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       34.85        18.28         8.94        19.99        21.01        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        58.59        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM 
       22.82        55.50        12.92        13.48        16.47         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ 
        8.71        13.41        83.24        33.11         7.59         5.06 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASX 
       53.95        15.78         2.89        20.02        16.44         8.98 
TCGA-VR-A8EQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       22.82        15.68        33.27         0.85        20.78         2.63 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        9.30         0.53         0.79        12.82         9.96         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49L 
        6.28        25.12         7.40        13.55        21.37        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       12.66        12.43        13.15        12.62        12.46        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       12.59        22.39         4.47        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU 
       13.18        13.38        13.18        12.03        12.26         5.16 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
       25.81        12.43         1.55        52.27        18.05         9.17 
TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.91        41.23        14.37         3.42         2.66 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.13              0.53 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            60.39            122.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           13.035            13.150 
[1] "0.1 - 60.4 (13.0)"  "0.5 - 122.1 (13.2)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         5        2        3        1        19        13
  7Q GAIN WILD-TYPE       3        3        3        0        28        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          10          4          5          5        3
  7Q GAIN WILD-TYPE        15         10          4          2        2
                   vv
clus                STAGE IVA
  7Q GAIN MUTATED           3
  7Q GAIN WILD-TYPE         1
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  5                 3
  STAGE IA                 2                 3
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               19                28
  STAGE IIB               13                18
  STAGE III               10                15
  STAGE IIIA               4                10
  STAGE IIIB               5                 4
  STAGE IIIC               5                 2
  STAGE IV                 3                 2
  STAGE IVA                3                 1
[1] 12  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                T0+T1 T2 T3 T4
  7Q GAIN MUTATED      19 15 43  0
  7Q GAIN WILD-TYPE    13 28 44  5
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              19                13
  T2                 15                28
  T3                 43                44
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7Q GAIN MUTATED   34 31  5  6
  7Q GAIN WILD-TYPE 43 37  7  2
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              34                43
  N1              31                37
  N2               5                 7
  N3               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   57  6
  7Q GAIN WILD-TYPE 78  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     57    6
  7Q GAIN WILD-TYPE   78    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              57                78
  1               6                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7 82
  7Q GAIN WILD-TYPE 20 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7   82
  7Q GAIN WILD-TYPE   20   75
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               7                20
  MALE                82                75
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   62 19
  7Q GAIN WILD-TYPE 62 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     62   19
  7Q GAIN WILD-TYPE   62   23
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               62                62
  YES              19                23
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   45 44
  7Q GAIN WILD-TYPE 43 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     45   44
  7Q GAIN WILD-TYPE   43   52
                                   clus
vv                                  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  45                43
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              44                52
[1] 2 2
[1] FALSE
D14V11, continuous
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   62  5  0  5
  7Q GAIN WILD-TYPE 75  7  2  2
D14V12, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              62                75
  R1               5                 7
  R2               0                 2
  RX               5                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED      23                         4    57
  7Q GAIN WILD-TYPE    23                         1    57
D14V14, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                  23                23
  BLACK OR AFRICAN AMERICAN               4                 1
  WHITE                                  57                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4 44
  7Q GAIN WILD-TYPE  2 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4   44
  7Q GAIN WILD-TYPE    2   44
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 2
  NOT HISPANIC OR LATINO              44                44
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   33 34
  8P GAIN WILD-TYPE 74 42
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               67               116 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               34                42 
$`8P GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-JY-A6F8 
       14.30         8.94        16.24         4.21        32.45       122.10 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A4ON 
       31.56         3.16        30.25        18.28        19.99        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y 
        1.38         3.16         4.90         7.13         2.60         0.36 
TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-R6-A6DQ 
       35.97        13.22         7.76        13.41        10.36         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE 
        5.06         7.04        15.78        12.69         7.00        16.44 
TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
       22.82        46.19        19.73        33.27        35.21        20.78 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93F 
       17.03        12.82         4.67        68.02         3.68        24.03 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G 
        0.30         4.31        47.93        13.55        21.37        10.85 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        5.92        10.45        13.41        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.25        12.62        12.59        12.85        12.03        13.18 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-Z6-A8JD 
       15.35        27.09         8.12        18.18        11.24         3.42 
TCGA-Z6-A8JE 
        2.10 

$`8P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 
        7.69         3.88        14.86        60.39        47.38        34.85 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       21.70        23.18        25.22         8.94        24.00        26.33 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
        4.70        32.61        21.01         3.32         7.17        58.59 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       29.00         7.43        22.82         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR 
        2.66        12.92        13.48        16.47         5.49         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW 
       27.12        83.24        52.57        46.09        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.99        16.31        38.40         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX 
        2.89         2.30        20.02         5.29         9.27         8.98 
TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       18.21        15.68         0.85         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
        9.30         0.53         0.79        23.41         9.96        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A88S TCGA-L5-A88W 
       12.16        44.75        41.52         6.28        15.48        25.12 
TCGA-L5-A88Z TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y 
        7.40        12.66        12.43        12.33        13.38        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.49        12.76        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        12.23        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO 
       12.85        12.26         5.16        20.38         3.42        25.81 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
       12.43         1.55        18.31        28.11        33.70        52.27 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       18.05         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.30              0.13 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           122.10             83.24 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            13.15             13.05 
[1] "0.3 - 122.1 (13.2)" "0.1 - 83.2 (13.1)" 
[1] "hr=" "1.6"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         2        2        2        1        15        10
  8P GAIN WILD-TYPE       6        3        4        0        32        21
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED          12          4          4          5        2
  8P GAIN WILD-TYPE        13         10          5          2        3
                   vv
clus                STAGE IVA
  8P GAIN MUTATED           2
  8P GAIN WILD-TYPE         2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 2                 4
  STAGE II                 1                 0
  STAGE IIA               15                32
  STAGE IIB               10                21
  STAGE III               12                13
  STAGE IIIA               4                10
  STAGE IIIB               4                 5
  STAGE IIIC               5                 2
  STAGE IV                 2                 3
  STAGE IVA                2                 2
[1] 12  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                T0+T1 T2 T3 T4
  8P GAIN MUTATED      10 11 40  1
  8P GAIN WILD-TYPE    22 32 47  4
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              10                22
  T2                 11                32
  T3                 40                47
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8P GAIN MUTATED   28 23  5  6
  8P GAIN WILD-TYPE 49 45  7  2
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              28                49
  N1              23                45
  N2               5                 7
  N3               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   46  4
  8P GAIN WILD-TYPE 89  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     46    4
  8P GAIN WILD-TYPE   89    5
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              46                89
  1               4                 5
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   10 58
  8P GAIN WILD-TYPE 17 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     10   58
  8P GAIN WILD-TYPE   17   99
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              10                17
  MALE                58                99
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   43 17
  8P GAIN WILD-TYPE 81 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     43   17
  8P GAIN WILD-TYPE   81   25
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               43                81
  YES              17                25
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   33 35
  8P GAIN WILD-TYPE 55 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     33   35
  8P GAIN WILD-TYPE   55   61
                                   clus
vv                                  8P GAIN MUTATED 8P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  33                55
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              35                61
[1] 2 2
[1] FALSE
D15V11, continuous
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED   49  7  0  3
  8P GAIN WILD-TYPE 88  5  2  4
D15V12, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              49                88
  R1               7                 5
  R2               0                 2
  RX               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED      17                         2    43
  8P GAIN WILD-TYPE    29                         3    71
D15V14, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                  17                29
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  43                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    1 30
  8P GAIN WILD-TYPE  5 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   30
  8P GAIN WILD-TYPE    5   58
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              30                58
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   58 42
  8Q GAIN WILD-TYPE 49 34
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              100                83 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               42                34 
$`8Q GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
       14.30        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C 
        7.69         3.88       122.10        23.18        31.56         3.16 
TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       30.25        18.28        19.99        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y 
        3.16         4.90         7.13         7.43         2.60         0.36 
TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       35.97        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
       27.12        46.09        10.36         7.59         5.06         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RE 
       53.95        15.78        12.69         7.00        20.02        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IG-A3I8 
        9.27         8.98        22.82        46.19        19.73        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A51D TCGA-IG-A625 
       35.21        20.78         2.63        20.12        17.03        12.82 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93F TCGA-L5-A43H 
        4.67        14.50        68.02         3.68        24.03         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K 
        4.31        47.93        13.55        21.37        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.59        13.25        12.62        12.59        12.59        12.85 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I1 
       11.54        12.33        12.23        12.03        13.18        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER 
       12.85        12.26        20.38        15.35        27.09        12.43 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
        8.12        33.70        18.18        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       41.23         3.42         2.10         1.32 

$`8Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-IG-A7DP 
       25.78        31.27        58.55         7.63         5.92        14.86 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-L5-A43M 
       60.39        47.38        34.85        21.70        25.22         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP 
       24.00        26.33         4.70        32.61        21.01         7.17 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       58.59        29.00        22.82         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV 
        2.66        12.92        13.48        16.47        83.24        52.57 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         7.82         7.99        16.31        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-X8-AAAR TCGA-IC-A6RF 
        9.30         2.89         2.30         5.29        18.21        15.68 
TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.85        18.64         9.30         0.53         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A88S 
        9.96        12.16        44.75        41.52         6.28        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A2 
       25.12         7.40        12.66        12.43        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.76        22.39        15.52        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       25.25        10.52        12.00        13.38         0.13        12.03 
TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
        5.16         3.42        25.81         1.55        18.31        28.11 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       52.27        18.05        25.08        14.37         2.66 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.30              0.13 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           122.10             83.24 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           12.835            13.480 
[1] "0.3 - 122.1 (12.8)" "0.1 - 83.2 (13.5)" 
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2        2        4        1        24        15
  8Q GAIN WILD-TYPE       6        3        2        0        23        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          18          8          6          7        2
  8Q GAIN WILD-TYPE         7          6          3          0        3
                   vv
clus                STAGE IVA
  8Q GAIN MUTATED           2
  8Q GAIN WILD-TYPE         2
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 4                 2
  STAGE II                 1                 0
  STAGE IIA               24                23
  STAGE IIB               15                16
  STAGE III               18                 7
  STAGE IIIA               8                 6
  STAGE IIIB               6                 3
  STAGE IIIC               7                 0
  STAGE IV                 2                 3
  STAGE IVA                2                 2
[1] 12  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                T0+T1 T2 T3 T4
  8Q GAIN MUTATED      12 19 58  3
  8Q GAIN WILD-TYPE    20 24 29  2
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              12                20
  T2                 19                24
  T3                 58                29
  T4                  3                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   39 37  7  8
  8Q GAIN WILD-TYPE 38 31  5  0
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              39                38
  N1              37                31
  N2               7                 5
  N3               8                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   74  4
  8Q GAIN WILD-TYPE 61  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     74    4
  8Q GAIN WILD-TYPE   61    5
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              74                61
  1               4                 5
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   14 87
  8Q GAIN WILD-TYPE 13 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14   87
  8Q GAIN WILD-TYPE   13   70
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              14                13
  MALE                87                70
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   63 27
  8Q GAIN WILD-TYPE 61 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     63   27
  8Q GAIN WILD-TYPE   61   15
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               63                61
  YES              27                15
[1] 2 2
[1] FALSE
D16V9, continuous
D16V10, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   47 54
  8Q GAIN WILD-TYPE 41 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     47   54
  8Q GAIN WILD-TYPE   41   42
                                   clus
vv                                  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  47                41
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              54                42
[1] 2 2
[1] FALSE
D16V11, continuous
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   75  9  1  3
  8Q GAIN WILD-TYPE 62  3  1  4
D16V12, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              75                62
  R1               9                 3
  R2               1                 1
  RX               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED      28                         2    61
  8Q GAIN WILD-TYPE    18                         3    53
D16V14, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                  28                18
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  61                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    2 50
  8Q GAIN WILD-TYPE  4 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2   50
  8Q GAIN WILD-TYPE    4   38
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              50                38
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED   12  4
  9P GAIN WILD-TYPE 95 72
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               167 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                72 
$`9P GAIN MUTATED`
TCGA-2H-A9GL TCGA-JY-A6F8 TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A8NT TCGA-IG-A625 
        5.92       122.10        29.00         0.36        27.12        12.82 
TCGA-L7-A56G TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A8I0 
       10.85        13.41        12.33        13.38        12.59        13.38 
TCGA-LN-A9FQ TCGA-VR-AA4G TCGA-VR-AA7D TCGA-Z6-AAPN 
       12.85        18.05         9.17         2.66 

$`9P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        8.94        16.24         4.21        32.45         7.69         3.88 
TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       14.86        60.39        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M 
       31.56        25.22         3.16        30.25        18.28         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00        26.33         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 
        4.90         7.13         7.43        22.82         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       83.24        52.57        46.09        10.36        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.99         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.02         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF 
        8.98        22.82        46.19        18.21        19.73        15.68 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ 
       47.93        15.48        25.12         7.40        13.55        21.37 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U 
        5.92        10.45        12.66        12.43        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        12.03        13.18        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO 
       12.26         5.16        20.38         3.42        15.35        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 
       33.70        18.18        52.27        11.24        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       41.23        14.37         3.42         2.10         1.32 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.36              0.13 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           122.10             83.24 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           12.835            13.180 
[1] "0.4 - 122.1 (12.8)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.7"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         1        0        0        0         7         1
  9P GAIN WILD-TYPE       7        5        6        1        40        30
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           2          1          1          1        0
  9P GAIN WILD-TYPE        23         13          8          6        5
                   vv
clus                STAGE IVA
  9P GAIN MUTATED           0
  9P GAIN WILD-TYPE         4
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                7                40
  STAGE IIB                1                30
  STAGE III                2                23
  STAGE IIIA               1                13
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  9P GAIN MUTATED       2  2 11  0
  9P GAIN WILD-TYPE    30 41 76  5
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               2                30
  T2                  2                41
  T3                 11                76
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9P GAIN MUTATED   10  2  2  1
  9P GAIN WILD-TYPE 67 66 10  7
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              10                67
  N1               2                66
  N2               2                10
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    14   0
  9P GAIN WILD-TYPE 121   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     14    0
  9P GAIN WILD-TYPE  121    9
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              14               121
  1               0                 9
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  15
  9P GAIN WILD-TYPE  26 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   15
  9P GAIN WILD-TYPE   26  142
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               1                26
  MALE                15               142
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     7   7
  9P GAIN WILD-TYPE 117  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      7    7
  9P GAIN WILD-TYPE  117   35
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                7               117
  YES               7                35
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    5 11
  9P GAIN WILD-TYPE 83 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5   11
  9P GAIN WILD-TYPE   83   85
                                   clus
vv                                  9P GAIN MUTATED 9P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   5                83
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              11                85
[1] 2 2
[1] FALSE
D17V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    13   2   0   0
  9P GAIN WILD-TYPE 124  10   2   7
D17V12, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              13               124
  R1               2                10
  R2               0                 2
  RX               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       7                         1     6
  9P GAIN WILD-TYPE    39                         4   108
D17V14, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   7                39
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   6               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    0  9
  9P GAIN WILD-TYPE  6 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    9
  9P GAIN WILD-TYPE    6   79
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               9                79
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   22 11
  9Q GAIN WILD-TYPE 85 65
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               33               150 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11                65 
$`9Q GAIN MUTATED`
TCGA-2H-A9GL TCGA-IC-A6RE TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43C TCGA-L5-A4OO 
        5.92         7.69       122.10        60.39         3.16         3.32 
TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A8NT TCGA-R6-A6L4 TCGA-S8-A6BV TCGA-VR-AA4D 
       29.00         0.36        27.12        16.31        20.02        46.19 
TCGA-IG-A50L TCGA-IG-A625 TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P 
        0.53        12.82        10.85         5.92        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       13.38        12.59        12.62        12.49        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-VR-A8ER TCGA-VR-AA4G 
        4.47        13.38        12.85        12.26        12.43        18.05 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-Z6-AAPN 
        9.17        25.08         2.66 

$`9Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A4QS TCGA-IG-A7DP 
        8.94        16.24         4.21        32.45         3.88        14.86 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       47.38        34.85        21.70        23.18        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25        18.28         8.94        24.00        26.33         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        19.99        21.01        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        3.16        58.59         4.90         7.13         7.43        22.82 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         3.75         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        83.24        52.57        46.09        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
       33.11         7.82         7.99         7.59         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        2.30        12.69         7.00         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 
        8.98        22.82        18.21        19.73        15.68        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
        9.30        17.03         0.79        23.41         9.96         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S 
       24.03         6.28         0.30         4.31        47.93        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49L TCGA-LN-A49M 
       25.12         7.40        13.55        21.37        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       12.43        13.15        15.35        13.25        12.46        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR 
       12.76        12.59        22.39        12.85        15.52        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FU TCGA-S8-A6BW 
       13.18        13.18         0.13        12.03         5.16        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU 
        3.42        15.35        25.81        27.09         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        8.12        28.11        33.70        18.18        52.27        11.24 
TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        41.23        14.37         3.42         2.10         1.32 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.36              0.13 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           122.10             83.24 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           12.490            13.235 
[1] "0.4 - 122.1 (12.5)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.2"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         2        0        0        0        11         5
  9Q GAIN WILD-TYPE       6        5        6        1        36        26
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           4          3          1          2        1
  9Q GAIN WILD-TYPE        21         11          8          5        4
                   vv
clus                STAGE IVA
  9Q GAIN MUTATED           0
  9Q GAIN WILD-TYPE         4
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA               11                36
  STAGE IIB                5                26
  STAGE III                4                21
  STAGE IIIA               3                11
  STAGE IIIB               1                 8
  STAGE IIIC               2                 5
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  9Q GAIN MUTATED       5  5 19  1
  9Q GAIN WILD-TYPE    27 38 68  4
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               5                27
  T2                  5                38
  T3                 19                68
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9Q GAIN MUTATED   15 11  2  2
  9Q GAIN WILD-TYPE 62 57 10  6
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              15                62
  N1              11                57
  N2               2                10
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    27   1
  9Q GAIN WILD-TYPE 108   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     27    1
  9Q GAIN WILD-TYPE  108    8
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              27               108
  1               1                 8
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  32
  9Q GAIN WILD-TYPE  26 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   32
  9Q GAIN WILD-TYPE   26  125
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               1                26
  MALE                32               125
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    17  12
  9Q GAIN WILD-TYPE 107  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     17   12
  9Q GAIN WILD-TYPE  107   30
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               17               107
  YES              12                30
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   12 21
  9Q GAIN WILD-TYPE 76 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     12   21
  9Q GAIN WILD-TYPE   76   75
                                   clus
vv                                  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  12                76
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              21                75
[1] 2 2
[1] FALSE
D18V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    26   3   1   0
  9Q GAIN WILD-TYPE 111   9   1   7
D18V12, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              26               111
  R1               3                 9
  R2               1                 1
  RX               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED      15                         2    13
  9Q GAIN WILD-TYPE    31                         3   101
D18V14, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                  15                31
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  13               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1 20
  9Q GAIN WILD-TYPE  5 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   20
  9Q GAIN WILD-TYPE    5   68
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              20                68
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   25 15
  10P GAIN WILD-TYPE 82 61
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                40                143 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                15                 61 
$`10P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-JY-A6F8 
       58.55        13.94        16.24        32.45         7.69       122.10 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A88V 
       25.22         3.16        18.28        32.61         3.16         2.60 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L7-A6VZ 
        3.02        55.50        12.92        16.47         8.71        10.36 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-V5-AASW TCGA-VR-AA4D 
        7.99         5.06         6.35        15.78         9.27        46.19 
TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3YC TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S 
       18.21        15.68        20.12        10.45        13.38        13.15 
TCGA-LN-A4A1 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-S8-A6BW TCGA-VR-A8ET 
       12.59        12.85        12.33        12.23        20.38         1.55 
TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.31        52.27         2.10         1.32 

$`10P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30         7.63         5.92         8.94 
TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 
        4.21         3.88        14.86        60.39        47.38        34.85 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE 
       21.70        23.18        31.56        30.25         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33         4.70        19.99        21.01        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG 
        7.43        22.82         0.36         3.75         2.66        35.97 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NT 
       13.48        13.22         7.76         5.49        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       83.24        52.57        46.09        33.11         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       16.31         7.04        38.40        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.02         5.29        16.44 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.98        22.82        19.73        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
        6.28         0.30         4.31        47.93        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M 
        7.40        13.55        21.37        10.85         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41        12.33        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       10.52        12.00        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-V5-A7RC 
        0.13        12.03        12.85        12.26         5.16         3.42 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX 
       15.35        25.81        27.09        12.43         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        18.18        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         2.66 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.32               0.13 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            122.10              83.24 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            13.035             13.180 
[1] "1.3 - 122.1 (13.0)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         4        2        1        1         6         5
  10P GAIN WILD-TYPE       4        3        5        0        41        26
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           4          6          0          1        2
  10P GAIN WILD-TYPE        21          8          9          6        3
                    vv
clus                 STAGE IVA
  10P GAIN MUTATED           2
  10P GAIN WILD-TYPE         2
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  2                  3
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                 6                 41
  STAGE IIB                 5                 26
  STAGE III                 4                 21
  STAGE IIIA                6                  8
  STAGE IIIB                0                  9
  STAGE IIIC                1                  6
  STAGE IV                  2                  3
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  10P GAIN MUTATED      12  7 16  0
  10P GAIN WILD-TYPE    20 36 71  5
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1               12                 20
  T2                   7                 36
  T3                  16                 71
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10P GAIN MUTATED   15 19  0  1
  10P GAIN WILD-TYPE 62 49 12  7
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               15                 62
  N1               19                 49
  N2                0                 12
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    25   4
  10P GAIN WILD-TYPE 110   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     25    4
  10P GAIN WILD-TYPE  110    5
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               25                110
  1                4                  5
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3  37
  10P GAIN WILD-TYPE  24 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3   37
  10P GAIN WILD-TYPE   24  120
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 37                120
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   28 10
  10P GAIN WILD-TYPE 96 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     28   10
  10P GAIN WILD-TYPE   96   32
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                28                 96
  YES               10                 32
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   25 15
  10P GAIN WILD-TYPE 63 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     25   15
  10P GAIN WILD-TYPE   63   81
                                   clus
vv                                  10P GAIN MUTATED 10P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   25                 63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               15                 81
[1] 2 2
[1] FALSE
D19V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    28   3   0   1
  10P GAIN WILD-TYPE 109   9   2   6
D19V12, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               28                109
  R1                3                  9
  R2                0                  2
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       7                         0    28
  10P GAIN WILD-TYPE    39                         5    86
D19V14, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    7                 39
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                   28                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    0 20
  10P GAIN WILD-TYPE  6 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   20
  10P GAIN WILD-TYPE    6   68
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               20                 68
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED   16 14
  10Q GAIN WILD-TYPE 91 62
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                30                153 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                 62 
$`10Q GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE TCGA-JY-A6F8 TCGA-JY-A93E 
       58.55        13.94        16.24         7.69       122.10        25.22 
TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ 
       32.61         3.16         3.02        55.50        12.92        16.47 
TCGA-L7-A6VZ TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-VR-A8EQ 
       10.36         7.99         5.06         6.35        15.78        22.82 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A5B8 TCGA-L5-A43J TCGA-LN-A49L 
       18.21        19.73        15.68         0.79         4.31        10.45 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A9FQ TCGA-S8-A6BW TCGA-VR-A8Q7 
       13.15        12.59        12.59        12.85        20.38        52.27 

$`10Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30         7.63         5.92         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH 
        4.21        32.45         3.88        14.86        60.39        47.38 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E 
       34.85        21.70        23.18        31.56         3.16        30.25 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
       18.28         8.94        24.00        26.33         4.70        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       21.01        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        22.82         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NL 
        0.36         3.75         2.66        35.97        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 
       52.57        46.09        33.11         7.82         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04        38.40        53.95         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.02         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-AA4D TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.98        46.19        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK 
        0.30        47.93        15.48        25.12         7.40        13.55 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       21.37        10.85         5.92        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.33        13.38        15.35        13.25        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-V5-A7RC 
       13.18         0.13        12.03        12.26         5.16         3.42 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35        25.81        27.09        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        33.70        18.18        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        2.10         1.32         2.66 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.79               0.13 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            122.10              83.24 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            13.545             12.850 
[1] "0.8 - 122.1 (13.5)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         4        2        2        0         5         4
  10Q GAIN WILD-TYPE       4        3        4        1        42        27
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           2          2          0          2        1
  10Q GAIN WILD-TYPE        23         12          9          5        4
                    vv
clus                 STAGE IVA
  10Q GAIN MUTATED           2
  10Q GAIN WILD-TYPE         2
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  2                  3
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                 5                 42
  STAGE IIB                 4                 27
  STAGE III                 2                 23
  STAGE IIIA                2                 12
  STAGE IIIB                0                  9
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  10Q GAIN MUTATED      10  3 14  0
  10Q GAIN WILD-TYPE    22 40 73  5
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1               10                 22
  T2                   3                 40
  T3                  14                 73
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10Q GAIN MUTATED   15 10  0  2
  10Q GAIN WILD-TYPE 62 58 12  6
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               15                 62
  N1               10                 58
  N2                0                 12
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    18   3
  10Q GAIN WILD-TYPE 117   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     18    3
  10Q GAIN WILD-TYPE  117    6
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               18                117
  1                3                  6
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  28
  10Q GAIN WILD-TYPE  25 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   28
  10Q GAIN WILD-TYPE   25  129
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                 28                129
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    22   5
  10Q GAIN WILD-TYPE 102  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     22    5
  10Q GAIN WILD-TYPE  102   37
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                22                102
  YES                5                 37
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   20 10
  10Q GAIN WILD-TYPE 68 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     20   10
  10Q GAIN WILD-TYPE   68   86
                                   clus
vv                                  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   20                 68
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               10                 86
[1] 2 2
[1] FALSE
D20V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    22   1   0   1
  10Q GAIN WILD-TYPE 115  11   2   6
D20V12, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               22                115
  R1                1                 11
  R2                0                  2
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       5                         0    22
  10Q GAIN WILD-TYPE    41                         5    92
D20V14, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    5                 41
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                   22                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V15, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    0 16
  10Q GAIN WILD-TYPE  6 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   16
  10Q GAIN WILD-TYPE    6   72
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               16                 72
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED   16 22
  11P GAIN WILD-TYPE 91 54
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                38                145 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                 54 
$`11P GAIN MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE 
        8.94        16.24       122.10        60.39         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A8NF TCGA-L5-A8NN 
       26.33        18.35         1.38        29.00         2.66         5.49 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 
       27.12        52.57        46.09         7.82         7.59         7.04 
TCGA-RE-A7BO TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FE 
        7.00        22.82        19.73        23.41        14.50         3.68 
TCGA-L5-A4OM TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4MQ 
       47.93         5.92        12.33        12.59        12.46        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A9FR TCGA-V5-A7RC TCGA-VR-A8EW TCGA-VR-A8EY 
       13.22         4.47        12.26         3.42         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-AA7I 
       18.18        15.91 

$`11P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
       13.94         4.21        32.45         7.69         3.88        14.86 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       47.38        34.85        21.70        23.18        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        3.16        30.25        18.28         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       21.01         3.32         7.17         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
        7.13         7.43        22.82         2.60         0.36         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
       13.22         7.76         8.71        13.41        83.24        10.36 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         7.99         5.06        16.31        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4D 
       20.02         5.29        16.44         9.27         8.98        46.19 
TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       18.21        15.68        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        12.82         9.96         4.67        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
       68.02        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G 
       15.48        25.12         7.40        13.55        21.37        10.85 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       15.35        13.25        12.62        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FU 
       13.38        13.18         0.13        12.03        12.85         5.16 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
       20.38        15.35        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.31        28.11        52.27        18.05        11.24         9.17 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.38               0.13 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            122.10              83.24 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            12.905             13.150 
[1] "1.4 - 122.1 (12.9)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.3"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         2        1        1        0        10         6
  11P GAIN WILD-TYPE       6        4        5        1        37        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           6          1          3          2        1
  11P GAIN WILD-TYPE        19         13          6          5        4
                    vv
clus                 STAGE IVA
  11P GAIN MUTATED           2
  11P GAIN WILD-TYPE         2
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                10                 37
  STAGE IIB                 6                 25
  STAGE III                 6                 19
  STAGE IIIA                1                 13
  STAGE IIIB                3                  6
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  11P GAIN MUTATED       7  5 23  1
  11P GAIN WILD-TYPE    25 38 64  4
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                7                 25
  T2                   5                 38
  T3                  23                 64
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11P GAIN MUTATED   16 12  5  2
  11P GAIN WILD-TYPE 61 56  7  6
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               16                 61
  N1               12                 56
  N2                5                  7
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    26   3
  11P GAIN WILD-TYPE 109   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     26    3
  11P GAIN WILD-TYPE  109    6
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               26                109
  1                3                  6
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6  33
  11P GAIN WILD-TYPE  21 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6   33
  11P GAIN WILD-TYPE   21  124
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                 33                124
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                  0  1
  11P GAIN MUTATED   30  6
  11P GAIN WILD-TYPE 94 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     30    6
  11P GAIN WILD-TYPE   94   36
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                30                 94
  YES                6                 36
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, binary
                    cls
clus                  0  1
  11P GAIN MUTATED   21 18
  11P GAIN WILD-TYPE 67 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     21   18
  11P GAIN WILD-TYPE   67   78
                                   clus
vv                                  11P GAIN MUTATED 11P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   21                 67
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               18                 78
[1] 2 2
[1] FALSE
D21V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    26   2   2   3
  11P GAIN WILD-TYPE 111  10   0   4
D21V12, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               26                111
  R1                2                 10
  R2                2                  0
  RX                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED      11                         1    24
  11P GAIN WILD-TYPE    35                         4    90
D21V14, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                   11                 35
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   24                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    0 17
  11P GAIN WILD-TYPE  6 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   17
  11P GAIN WILD-TYPE    6   71
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               17                 71
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED   16 13
  11Q GAIN WILD-TYPE 91 63
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                154 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 63 
$`11Q GAIN MUTATED`
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH 
      122.10        60.39         8.94        24.00        26.33        32.61 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A8NN TCGA-Q9-A6FW 
       18.35         1.38        29.00         0.36         5.49         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-V5-AASW TCGA-VR-A8EQ 
        7.59         7.04        15.78         7.00         9.27        22.82 
TCGA-ZR-A9CJ TCGA-IG-A51D TCGA-IG-A97H TCGA-JY-A6FE TCGA-LN-A49K TCGA-LN-A49Y 
       19.73        17.03        14.50         3.68         5.92        12.46 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A9FR TCGA-VR-A8EW TCGA-VR-A8EY 
       12.33        13.22        12.26         8.12        33.70 

$`11Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.88        14.86        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OG 
       31.56        25.22         3.16        30.25        18.28         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       19.99        21.01         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 
        4.90         7.13         7.43        22.82         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       16.47        13.22         7.76         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DN 
       83.24        52.57        46.09        10.36        33.11         7.99 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31        38.40         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         2.30        12.69        20.02         5.29        16.44 
TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.98        46.19        18.21        15.68        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.53         0.79        23.41        12.82         9.96         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       12.16        44.75        68.02        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        0.30         4.31        47.93        15.48        25.12         7.40 
TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       13.55        21.37        10.85        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 
       22.39        12.85        15.52        11.54         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FU 
       13.38        13.18         0.13        12.03        12.85         5.16 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       20.38         3.42        15.35        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        1.55        18.31        28.11        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        3.42         2.10         1.32         2.66 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.36               0.13 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            122.10              83.24 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            12.460             13.165 
[1] "0.4 - 122.1 (12.5)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         3        0        0        0         6         5
  11Q GAIN WILD-TYPE       5        5        6        1        41        26
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           4          1          3          1        0
  11Q GAIN WILD-TYPE        21         13          6          6        5
                    vv
clus                 STAGE IVA
  11Q GAIN MUTATED           1
  11Q GAIN WILD-TYPE         3
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  0                  5
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 6                 41
  STAGE IIB                 5                 26
  STAGE III                 4                 21
  STAGE IIIA                1                 13
  STAGE IIIB                3                  6
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  11Q GAIN MUTATED       8  3 15  0
  11Q GAIN WILD-TYPE    24 40 72  5
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                 24
  T2                   3                 40
  T3                  15                 72
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11Q GAIN MUTATED    9 10  5  1
  11Q GAIN WILD-TYPE 68 58  7  7
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                9                 68
  N1               10                 58
  N2                5                  7
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    18   1
  11Q GAIN WILD-TYPE 117   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     18    1
  11Q GAIN WILD-TYPE  117    8
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               18                117
  1                1                  8
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  25
  11Q GAIN WILD-TYPE  23 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   25
  11Q GAIN WILD-TYPE   23  132
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                4                 23
  MALE                 25                132
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    22   3
  11Q GAIN WILD-TYPE 102  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     22    3
  11Q GAIN WILD-TYPE  102   39
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                22                102
  YES                3                 39
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   19 10
  11Q GAIN WILD-TYPE 69 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     19   10
  11Q GAIN WILD-TYPE   69   86
                                   clus
vv                                  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   19                 69
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               10                 86
[1] 2 2
[1] FALSE
D22V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    20   0   0   4
  11Q GAIN WILD-TYPE 117  12   2   3
D22V12, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               20                117
  R1                0                 12
  R2                0                  2
  RX                4                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       7                         0    21
  11Q GAIN WILD-TYPE    39                         5    93
D22V14, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    7                 39
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                   21                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V15, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    0 14
  11Q GAIN WILD-TYPE  6 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   14
  11Q GAIN WILD-TYPE    6   74
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               14                 74
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   35 22
  12P GAIN WILD-TYPE 72 54
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                57                126 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                22                 54 
$`12P GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4OO TCGA-L5-A4OT 
        7.63        16.24        24.00        19.99         3.32         4.90 
TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L7-A6VZ 
        0.36         2.66        13.22         5.49        27.12        10.36 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-IG-A3QL 
        7.99         7.59        38.40        53.95        12.69        35.21 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-L5-A43H 
        2.63        18.64         0.53        23.41         4.67         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
        4.31        47.93        21.37        10.85         5.92        10.45 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 
       12.33        13.38        13.15        12.59        13.25        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.76        12.59        12.85        15.52        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-S8-A6BW 
       12.33        25.25        13.18        13.18         0.13        20.38 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 
       27.09         1.55        18.31         8.12        28.11        52.27 
TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       14.37         1.32         2.66 

$`12P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
        8.94         4.21        32.45         7.69         3.88        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M 
       31.56        25.22         3.16        30.25        18.28         8.94 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP 
       26.33         4.70        32.61        21.01        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG 
       22.82         2.60         3.75         3.02        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       12.92        13.48        16.47         7.76         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ 
       83.24        52.57        46.09        33.11         7.82         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       16.31         7.04         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        2.30         7.00        20.02         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF 
        8.98        22.82        46.19        18.21        19.73        15.68 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D 
       33.27         0.85        20.78        20.12         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        12.82         9.96        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A88S 
       68.02         3.68        41.52        24.03         6.28        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       25.12         7.40        13.55        12.66        12.43        13.41 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 
       15.35        12.62        12.46        12.49        22.39        11.54 
TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 
       12.33        10.52        12.00        12.23        12.03        13.38 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-V5-AASV 
       12.03        12.85        12.26         5.16         3.42        15.35 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
       25.81        12.43        33.70        18.18        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        15.91        25.08        41.23         3.42         2.10 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.13               0.79 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             53.95             122.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            12.690             13.445 
[1] "0.1 - 54.0 (12.7)"  "0.8 - 122.1 (13.4)"
[1] "hr=" "1.2"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         0        1        1        1        17         6
  12P GAIN WILD-TYPE       8        4        5        0        30        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           8          4          4          3        3
  12P GAIN WILD-TYPE        17         10          5          4        2
                    vv
clus                 STAGE IVA
  12P GAIN MUTATED           3
  12P GAIN WILD-TYPE         1
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                17                 30
  STAGE IIB                 6                 25
  STAGE III                 8                 17
  STAGE IIIA                4                 10
  STAGE IIIB                4                  5
  STAGE IIIC                3                  4
  STAGE IV                  3                  2
  STAGE IVA                 3                  1
[1] 12  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                 T0+T1 T2 T3 T4
  12P GAIN MUTATED       6 15 31  0
  12P GAIN WILD-TYPE    26 28 56  5
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1                6                 26
  T2                  15                 28
  T3                  31                 56
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  12P GAIN MUTATED   25 20  4  3
  12P GAIN WILD-TYPE 52 48  8  5
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               25                 52
  N1               20                 48
  N2                4                  8
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   39  6
  12P GAIN WILD-TYPE 96  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     39    6
  12P GAIN WILD-TYPE   96    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               39                 96
  1                6                  3
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     4  54
  12P GAIN WILD-TYPE  23 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4   54
  12P GAIN WILD-TYPE   23  103
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                4                 23
  MALE                 54                103
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   33 17
  12P GAIN WILD-TYPE 91 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     33   17
  12P GAIN WILD-TYPE   91   25
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                33                 91
  YES               17                 25
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   17 41
  12P GAIN WILD-TYPE 71 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     17   41
  12P GAIN WILD-TYPE   71   55
                                   clus
vv                                  12P GAIN MUTATED 12P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   17                 71
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               41                 55
[1] 2 2
[1] FALSE
D23V11, continuous
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED   42  4  1  2
  12P GAIN WILD-TYPE 95  8  1  5
D23V12, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               42                 95
  R1                4                  8
  R2                1                  1
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED      23                         2    30
  12P GAIN WILD-TYPE    23                         3    84
D23V14, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                   23                 23
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                   30                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2 34
  12P GAIN WILD-TYPE  4 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   34
  12P GAIN WILD-TYPE    4   54
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               34                 54
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   22 15
  12Q GAIN WILD-TYPE 85 61
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                37                146 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                 61 
$`12Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A88Y 
        7.63        16.24        24.00         3.32         4.90         0.36 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-R6-A6DQ 
       13.22         5.49        27.12        52.57        10.36         7.59 
TCGA-R6-A6XG TCGA-R6-A8WG TCGA-ZR-A9CJ TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A8O2 
       38.40        12.69        19.73         2.63         0.53         4.67 
TCGA-L5-A4OM TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A6 
       47.93        10.45        12.59        13.25        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        12.33         4.47        12.33        25.25 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 
       13.18         0.13        27.09        18.31        28.11        52.27 
TCGA-Z6-AAPN 
        2.66 

$`12Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
        8.94         4.21        32.45         7.69         3.88        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M 
       31.56        25.22         3.16        30.25        18.28         8.94 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       26.33         4.70        32.61        19.99        21.01        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        7.43        22.82         2.60         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM 
        2.66        35.97        12.92        13.48        16.47         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW 
        8.71        13.41        83.24        46.09        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.99         5.06        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         2.89         2.30         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
        5.29        16.44         9.27         8.98        22.82        46.19 
TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       18.21        15.68        33.27        35.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12        18.64         9.30        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       12.82         9.96        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G 
       15.48        25.12         7.40        13.55        21.37        10.85 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
        5.92        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.59        22.39        13.22        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.03        13.18        13.38        12.03        12.85        12.26 
TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER 
        5.16        20.38         3.42        15.35        25.81        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
        1.55         8.12        33.70        18.18        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB 
        2.10         1.32 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.13               0.30 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             52.57             122.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             12.59              13.30 
[1] "0.1 - 52.6 (12.6)"  "0.3 - 122.1 (13.3)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0        1        0        1        11         2
  12Q GAIN WILD-TYPE       8        4        6        0        36        29
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           5          3          3          3        3
  12Q GAIN WILD-TYPE        20         11          6          4        2
                    vv
clus                 STAGE IVA
  12Q GAIN MUTATED           2
  12Q GAIN WILD-TYPE         2
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  1                  4
  STAGE IB                  0                  6
  STAGE II                  1                  0
  STAGE IIA                11                 36
  STAGE IIB                 2                 29
  STAGE III                 5                 20
  STAGE IIIA                3                 11
  STAGE IIIB                3                  6
  STAGE IIIC                3                  4
  STAGE IV                  3                  2
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  12Q GAIN MUTATED       4  9 22  0
  12Q GAIN WILD-TYPE    28 34 65  5
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                4                 28
  T2                   9                 34
  T3                  22                 65
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  12Q GAIN MUTATED   15 14  3  3
  12Q GAIN WILD-TYPE 62 54  9  5
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               15                 62
  N1               14                 54
  N2                3                  9
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    25   5
  12Q GAIN WILD-TYPE 110   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     25    5
  12Q GAIN WILD-TYPE  110    4
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               25                110
  1                5                  4
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3  35
  12Q GAIN WILD-TYPE  24 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   35
  12Q GAIN WILD-TYPE   24  122
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 35                122
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    23   9
  12Q GAIN WILD-TYPE 101  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     23    9
  12Q GAIN WILD-TYPE  101   33
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                23                101
  YES                9                 33
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   15 23
  12Q GAIN WILD-TYPE 73 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     15   23
  12Q GAIN WILD-TYPE   73   73
                                   clus
vv                                  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   15                 73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               23                 73
[1] 2 2
[1] FALSE
D24V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    28   3   1   1
  12Q GAIN WILD-TYPE 109   9   1   6
D24V12, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               28                109
  R1                3                  9
  R2                1                  1
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED      16                         0    19
  12Q GAIN WILD-TYPE    30                         5    95
D24V14, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                   16                 30
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                   19                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1 21
  12Q GAIN WILD-TYPE  5 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   21
  12Q GAIN WILD-TYPE    5   67
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               21                 67
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   22 21
  13Q GAIN WILD-TYPE 85 55
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                43                140 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                 55 
$`13Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-JY-A6F8 TCGA-JY-A6FH 
       31.27        14.30         5.92        13.94       122.10        47.38 
TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M 
       23.18        31.56         3.16        30.25        18.28         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A88V 
        4.70        19.99         7.17         1.38         7.13         2.60 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NT TCGA-Q9-A6FW 
        0.36         3.02         2.66        12.92        27.12         7.82 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB 
       16.31         7.04         9.30        15.78        20.02         5.29 
TCGA-V5-AASW TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IG-A5B8 TCGA-IG-A97H 
        9.27        46.19        18.21        19.73         0.79        14.50 
TCGA-JY-A6FE TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FQ TCGA-V5-A7RC 
        3.68        12.33        25.25        12.00        12.85         3.42 
TCGA-XP-A8T6 
       25.08 

$`13Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        58.55         7.63         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A938 
       32.45         7.69         3.88        14.86        60.39        34.85 
TCGA-JY-A939 TCGA-JY-A93E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       21.70        25.22        24.00        26.33        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI 
        7.43        22.82         3.75        55.50        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DN 
       83.24        52.57        46.09        10.36        33.11         7.99 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 
        7.59         5.06        38.40         6.35        53.95         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ 
        2.30        12.69         7.00        16.44         8.98        22.82 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       15.68        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.12        18.64         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       12.82         9.96         4.67        12.16        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM 
       41.52        24.03         6.28         0.30         4.31        47.93 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G 
       15.48        25.12         7.40        13.55        21.37        10.85 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        15.52        11.54        13.22         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       10.52        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV 
        0.13        12.03        12.26         5.16        20.38        15.35 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        15.91        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.36               0.13 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            122.10              83.24 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             12.85              13.18 
[1] "0.4 - 122.1 (12.8)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.4"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         4        1        1        0         4         7
  13Q GAIN WILD-TYPE       4        4        5        1        43        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           5          3          2          3        1
  13Q GAIN WILD-TYPE        20         11          7          4        4
                    vv
clus                 STAGE IVA
  13Q GAIN MUTATED           2
  13Q GAIN WILD-TYPE         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 4                 43
  STAGE IIB                 7                 24
  STAGE III                 5                 20
  STAGE IIIA                3                 11
  STAGE IIIB                2                  7
  STAGE IIIC                3                  4
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  13Q GAIN MUTATED      13  7 17  0
  13Q GAIN WILD-TYPE    19 36 70  5
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               13                 19
  T2                   7                 36
  T3                  17                 70
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  13Q GAIN MUTATED   13 16  4  3
  13Q GAIN WILD-TYPE 64 52  8  5
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               13                 64
  N1               16                 52
  N2                4                  8
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    23   3
  13Q GAIN WILD-TYPE 112   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     23    3
  13Q GAIN WILD-TYPE  112    6
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               23                112
  1                3                  6
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5  38
  13Q GAIN WILD-TYPE  22 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   38
  13Q GAIN WILD-TYPE   22  119
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                5                 22
  MALE                 38                119
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   33  6
  13Q GAIN WILD-TYPE 91 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     33    6
  13Q GAIN WILD-TYPE   91   36
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                33                 91
  YES                6                 36
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   34  9
  13Q GAIN WILD-TYPE 54 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     34    9
  13Q GAIN WILD-TYPE   54   87
                                   clus
vv                                  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   34                 54
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                9                 87
[1] 2 2
[1] FALSE
D25V11, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    30   3   0   2
  13Q GAIN WILD-TYPE 107   9   2   5
D25V12, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               30                107
  R1                3                  9
  R2                0                  2
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       6                         2    28
  13Q GAIN WILD-TYPE    40                         3    86
D25V14, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    6                 40
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                   28                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V15, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3 15
  13Q GAIN WILD-TYPE  3 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3   15
  13Q GAIN WILD-TYPE    3   73
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  3
  NOT HISPANIC OR LATINO               15                 73
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   30 17
  14Q GAIN WILD-TYPE 77 59
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                47                136 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                17                 59 
$`14Q GAIN MUTATED`
TCGA-2H-A9GL TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OR TCGA-L5-A4OX 
        5.92        23.18         3.16        30.25         3.16         7.43 
TCGA-L5-A8NG TCGA-L5-A8NN TCGA-L5-A8NS TCGA-R6-A6DN TCGA-R6-A6Y0 TCGA-S8-A6BV 
       35.97         5.49        13.41         7.99        53.95        20.02 
TCGA-V5-AASX TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
        8.98        46.19        19.73         0.85        20.78        18.64 
TCGA-IG-A6QS TCGA-IG-A97I TCGA-L5-A43J TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49S 
        9.96        12.16         4.31        21.37         5.92        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A9 
       15.35        12.59        12.62        12.59        12.59        11.54 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       13.22        12.33        25.25        12.03        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-S8-A6BW TCGA-VR-A8EW TCGA-VR-AA7B TCGA-VR-AA7D 
       12.03        12.26        20.38         8.12        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        25.08         3.42         2.10         1.32 

$`14Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        8.94        16.24         4.21        32.45         7.69         3.88 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       14.86       122.10        60.39        47.38        34.85        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       31.56        25.22        18.28         8.94        24.00        26.33 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        4.70        32.61        19.99        21.01        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38        58.59         4.90        29.00         7.13 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       22.82         2.60         0.36         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        27.12        83.24        52.57        46.09        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EQ 
       12.69         7.00         5.29        16.44         9.27        22.82 
TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC 
       18.21        15.68        33.27        35.21         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        44.75        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
       24.03         6.28         0.30        47.93        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        7.40        13.55        10.85        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
       13.41        12.33        13.38        13.25        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.76        22.39        12.85        15.52        12.33         4.47 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ 
       10.52        12.00        12.23        13.38        13.18        12.85 
TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
        5.16         3.42        15.35        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       18.05        41.23        14.37         2.66 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.13               0.30 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             53.95             122.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            12.330             13.395 
[1] "0.1 - 54.0 (12.3)"  "0.3 - 122.1 (13.4)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         1        1        1        0        15        10
  14Q GAIN WILD-TYPE       7        4        5        1        32        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           6          5          2          2        1
  14Q GAIN WILD-TYPE        19          9          7          5        4
                    vv
clus                 STAGE IVA
  14Q GAIN MUTATED           0
  14Q GAIN WILD-TYPE         4
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                15                 32
  STAGE IIB                10                 21
  STAGE III                 6                 19
  STAGE IIIA                5                  9
  STAGE IIIB                2                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  14Q GAIN MUTATED       3 16 22  3
  14Q GAIN WILD-TYPE    29 27 65  2
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                3                 29
  T2                  16                 27
  T3                  22                 65
  T4                   3                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  14Q GAIN MUTATED   24 15  2  3
  14Q GAIN WILD-TYPE 53 53 10  5
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               24                 53
  N1               15                 53
  N2                2                 10
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   38  1
  14Q GAIN WILD-TYPE 97  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     38    1
  14Q GAIN WILD-TYPE   97    8
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               38                 97
  1                1                  8
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  46
  14Q GAIN WILD-TYPE  25 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   46
  14Q GAIN WILD-TYPE   25  111
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                 46                111
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   32 13
  14Q GAIN WILD-TYPE 92 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     32   13
  14Q GAIN WILD-TYPE   92   29
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                32                 92
  YES               13                 29
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   15 33
  14Q GAIN WILD-TYPE 73 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   33
  14Q GAIN WILD-TYPE   73   63
                                   clus
vv                                  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   15                 73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               33                 63
[1] 2 2
[1] FALSE
D26V11, continuous
                    vv
clus                 R0 R1 R2 RX
  14Q GAIN MUTATED   39  1  1  2
  14Q GAIN WILD-TYPE 98 11  1  5
D26V12, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               39                 98
  R1                1                 11
  R2                1                  1
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED      19                         1    26
  14Q GAIN WILD-TYPE    27                         4    88
D26V14, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                   19                 27
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   26                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V15, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    1 31
  14Q GAIN WILD-TYPE  5 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   31
  14Q GAIN WILD-TYPE    5   57
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               31                 57
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   16 13
  15Q GAIN WILD-TYPE 91 63
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                29                154 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                13                 63 
$`15Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43C TCGA-L5-A4OR 
        7.63         8.94       122.10        60.39         3.16         3.16 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NW TCGA-M9-A5M8 
        7.13         2.60         0.36        16.47        46.09        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-VR-A8EQ TCGA-IG-A50L 
        7.82         7.59         7.04         6.35        22.82         0.53 
TCGA-L5-A88S TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4MR TCGA-LN-A7HW 
       15.48        10.85        10.45        13.38        13.22        12.00 
TCGA-LN-A7HX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-AA7D TCGA-XP-A8T7 
       12.23        27.09         1.55         9.17        41.23 

$`15Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
       16.24         4.21        32.45         7.69         3.88        14.86 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       47.38        34.85        21.70        23.18        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25        18.28         8.94        24.00        26.33         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T 
        1.38        58.59         4.90        29.00         7.43        22.82 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.75         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-R6-A6DN TCGA-R6-A6KZ 
       27.12        83.24        52.57        10.36         7.99         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       16.31        38.40        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.02         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF 
        9.27         8.98        46.19        18.21        19.73        15.68 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
       18.64         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K 
       47.93        25.12         7.40        13.55        21.37         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY 
       12.33         4.47        12.33        25.25        10.52        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO 
       12.26         5.16        20.38         3.42        15.35        25.81 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 
       52.27        18.05        11.24        15.91        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        3.42         2.10         1.32         2.66 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.36               0.13 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            122.10              83.24 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            10.450             13.235 
[1] "0.4 - 122.1 (10.4)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.2"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         2        1        2        0         8         1
  15Q GAIN WILD-TYPE       6        4        4        1        39        30
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           6          1          2          1        0
  15Q GAIN WILD-TYPE        19         13          7          6        5
                    vv
clus                 STAGE IVA
  15Q GAIN MUTATED           0
  15Q GAIN WILD-TYPE         4
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  4
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                 8                 39
  STAGE IIB                 1                 30
  STAGE III                 6                 19
  STAGE IIIA                1                 13
  STAGE IIIB                2                  7
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  15Q GAIN MUTATED       4  9 12  0
  15Q GAIN WILD-TYPE    28 34 75  5
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1                4                 28
  T2                   9                 34
  T3                  12                 75
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  15Q GAIN MUTATED   13  9  2  1
  15Q GAIN WILD-TYPE 64 59 10  7
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               13                 64
  N1                9                 59
  N2                2                 10
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    21   0
  15Q GAIN WILD-TYPE 114   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     21    0
  15Q GAIN WILD-TYPE  114    9
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               21                114
  1                0                  9
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3  27
  15Q GAIN WILD-TYPE  24 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   27
  15Q GAIN WILD-TYPE   24  130
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 27                130
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    21   6
  15Q GAIN WILD-TYPE 103  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     21    6
  15Q GAIN WILD-TYPE  103   36
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                21                103
  YES                6                 36
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   17 13
  15Q GAIN WILD-TYPE 71 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     17   13
  15Q GAIN WILD-TYPE   71   83
                                   clus
vv                                  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   17                 71
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               13                 83
[1] 2 2
[1] FALSE
D27V11, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    25   0   0   1
  15Q GAIN WILD-TYPE 112  12   2   6
D27V12, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               25                112
  R1                0                 12
  R2                0                  2
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       7                         1    17
  15Q GAIN WILD-TYPE    39                         4    97
D27V14, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    7                 39
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   17                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    1 12
  15Q GAIN WILD-TYPE  5 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   12
  15Q GAIN WILD-TYPE    5   76
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               12                 76
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   25 16
  16P GAIN WILD-TYPE 82 60
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                41                142 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                 60 
$`16P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NS 
       58.55         3.32        29.00        55.50         2.66        13.41 
TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-ZR-A9CJ 
       27.12        10.36         5.06        38.40        15.78        19.73 
TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-L5-A43H 
        0.85         0.53         0.79         4.67        14.50         0.30 
TCGA-L5-A88S TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A1 
       15.48        21.37         5.92        13.15        13.25        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HY 
       12.76        12.59        12.85        11.54        12.33        12.03 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8ER 
       13.18         0.13        12.85        20.38        15.35        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        8.12        28.11        25.08        14.37         3.42 

$`16P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        8.94        16.24         4.21        32.45         7.69         3.88 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       14.86       122.10        60.39        47.38        34.85        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I 
       23.18        31.56        25.22         3.16        30.25        18.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00        26.33         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y 
        4.90         7.13         7.43        22.82         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         7.76         5.49         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       46.09        33.11         7.82         7.99         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04         6.35        53.95         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.02         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3I8 
        8.98        22.82        46.19        18.21        15.68        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       35.21        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FA 
       17.03        23.41        12.82         9.96        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J 
       68.02         3.68        41.52        24.03         6.28         4.31 
TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L7-A56G TCGA-LN-A49L 
       47.93        25.12         7.40        13.55        10.85        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.38        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        12.62        12.46        12.49        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU 
       12.23        13.18        13.38        12.03        12.26         5.16 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
        3.42        25.81        27.09         1.55        18.31        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23         2.10         1.32         2.66 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.13               0.36 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             58.55             122.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             12.85              13.22 
[1] "0.1 - 58.5 (12.8)"  "0.4 - 122.1 (13.2)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         1        0        3        1        10         8
  16P GAIN WILD-TYPE       7        5        3        0        37        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           6          2          2          3        0
  16P GAIN WILD-TYPE        19         12          7          4        5
                    vv
clus                 STAGE IVA
  16P GAIN MUTATED           3
  16P GAIN WILD-TYPE         1
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                10                 37
  STAGE IIB                 8                 23
  STAGE III                 6                 19
  STAGE IIIA                2                 12
  STAGE IIIB                2                  7
  STAGE IIIC                3                  4
  STAGE IV                  0                  5
  STAGE IVA                 3                  1
[1] 12  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                 T0+T1 T2 T3 T4
  16P GAIN MUTATED       4  9 24  2
  16P GAIN WILD-TYPE    28 34 63  3
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                4                 28
  T2                   9                 34
  T3                  24                 63
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16P GAIN MUTATED   20 13  2  3
  16P GAIN WILD-TYPE 57 55 10  5
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               20                 57
  N1               13                 55
  N2                2                 10
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    31   3
  16P GAIN WILD-TYPE 104   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     31    3
  16P GAIN WILD-TYPE  104    6
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               31                104
  1                3                  6
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  40
  16P GAIN WILD-TYPE  26 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   40
  16P GAIN WILD-TYPE   26  117
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                1                 26
  MALE                 40                117
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   25 12
  16P GAIN WILD-TYPE 99 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     25   12
  16P GAIN WILD-TYPE   99   30
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                25                 99
  YES               12                 30
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   12 29
  16P GAIN WILD-TYPE 76 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12   29
  16P GAIN WILD-TYPE   76   67
                                   clus
vv                                  16P GAIN MUTATED 16P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   12                 76
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               29                 67
[1] 2 2
[1] FALSE
D28V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    33   3   0   0
  16P GAIN WILD-TYPE 104   9   2   7
D28V12, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               33                104
  R1                3                  9
  R2                0                  2
  RX                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED      17                         3    18
  16P GAIN WILD-TYPE    29                         2    96
D28V14, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                   17                 29
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   18                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2 25
  16P GAIN WILD-TYPE  4 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   25
  16P GAIN WILD-TYPE    4   63
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               25                 63
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   22 16
  16Q GAIN WILD-TYPE 85 60
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                38                145 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                 60 
$`16Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A8NF TCGA-L5-A8NS TCGA-L5-A8NT 
       13.94         3.32        29.00         2.66        13.41        27.12 
TCGA-L5-A8NV TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-ZR-A9CJ TCGA-IG-A3Y9 TCGA-IG-A5B8 
       52.57        38.40        15.78        19.73         0.85         0.79 
TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88S TCGA-L5-A8NQ TCGA-LN-A49R 
        4.67         0.30         4.31        15.48        21.37        13.38 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 
       12.59        12.76        12.59        12.85        11.54        12.33 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-S8-A6BW TCGA-V5-A7RC 
       12.03        13.18         0.13        12.85        20.38         3.42 
TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA7B TCGA-XP-A8T8 
       15.35        12.43         8.12        28.11        11.24        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE 
        3.42         2.10 

$`16Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        8.94        16.24         4.21        32.45         7.69         3.88 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       14.86       122.10        60.39        47.38        34.85        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I 
       23.18        31.56        25.22         3.16        30.25        18.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00        26.33         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y 
        4.90         7.13         7.43        22.82         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU 
       16.47        13.22         7.76         5.49         8.71        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       46.09        10.36        33.11         7.82         7.99         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR 
       16.44         9.27         8.98        22.82        46.19        18.21 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       15.68        33.27        35.21        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
       18.64         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        9.96        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z 
       41.52        24.03         6.28        47.93        25.12         7.40 
TCGA-L5-A8NK TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       13.55        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.62        12.46        12.49        22.39        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-VR-A8EO 
       13.18        13.38        12.03        12.26         5.16        25.81 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       27.09         1.55        18.31        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A9VB 
       18.05         9.17        15.91        25.08        41.23         1.32 
TCGA-Z6-AAPN 
        2.66 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.13               0.36 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             52.57             122.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            12.675             13.220 
[1] "0.1 - 52.6 (12.7)"  "0.4 - 122.1 (13.2)"
[1] "hr=" "1.4"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0        0        3        1         8         8
  16Q GAIN WILD-TYPE       8        5        3        0        39        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           6          2          2          2        1
  16Q GAIN WILD-TYPE        19         12          7          5        4
                    vv
clus                 STAGE IVA
  16Q GAIN MUTATED           3
  16Q GAIN WILD-TYPE         1
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                 8                 39
  STAGE IIB                 8                 23
  STAGE III                 6                 19
  STAGE IIIA                2                 12
  STAGE IIIB                2                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 3                  1
[1] 12  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                 T0+T1 T2 T3 T4
  16Q GAIN MUTATED       4  7 23  2
  16Q GAIN WILD-TYPE    28 36 64  3
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                4                 28
  T2                   7                 36
  T3                  23                 64
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16Q GAIN MUTATED   19 12  2  3
  16Q GAIN WILD-TYPE 58 56 10  5
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               19                 58
  N1               12                 56
  N2                2                 10
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    27   4
  16Q GAIN WILD-TYPE 108   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     27    4
  16Q GAIN WILD-TYPE  108    5
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               27                108
  1                4                  5
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2  36
  16Q GAIN WILD-TYPE  25 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   36
  16Q GAIN WILD-TYPE   25  121
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                 36                121
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    24  11
  16Q GAIN WILD-TYPE 100  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     24   11
  16Q GAIN WILD-TYPE  100   31
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                24                100
  YES               11                 31
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   10 28
  16Q GAIN WILD-TYPE 78 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10   28
  16Q GAIN WILD-TYPE   78   68
                                   clus
vv                                  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   10                 78
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               28                 68
[1] 2 2
[1] FALSE
D29V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    29   3   0   2
  16Q GAIN WILD-TYPE 108   9   2   5
D29V12, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               29                108
  R1                3                  9
  R2                0                  2
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED      13                         3    19
  16Q GAIN WILD-TYPE    33                         2    95
D29V14, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                   13                 33
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   19                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    1 22
  16Q GAIN WILD-TYPE  5 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   22
  16Q GAIN WILD-TYPE    5   66
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               22                 66
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   21 12
  17P GAIN WILD-TYPE 86 64
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                33                150 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                 64 
$`17P GAIN MUTATED`
TCGA-IC-A6RE TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43I TCGA-L5-A4ON 
        7.69        60.39        23.18        25.22        18.28        18.35 
TCGA-L5-A4OQ TCGA-L5-A8NE TCGA-L5-A8NG TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-VR-AA4D 
        1.38        55.50        35.97         7.99         5.06        46.19 
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88Z 
       35.21         0.53        17.03         0.30         4.31         7.40 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A7HW 
       13.41        13.38        12.59        12.49        12.59        12.00 
TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-V5-A7RC TCGA-VR-A8ET TCGA-VR-A8EU 
       13.18        12.85        12.26         3.42         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-AA7I TCGA-Z6-A8JE 
       33.70        15.91         2.10 

$`17P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A4QS 
       13.94         8.94        16.24         4.21        32.45         3.88 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
       14.86       122.10        47.38        34.85        21.70        31.56 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16        30.25         8.94        24.00        26.33         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       32.61        19.99        21.01         3.32         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
       58.59         4.90        29.00         7.13         7.43        22.82 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         0.36         3.75         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       13.48        16.47        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         7.82         7.59        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.02         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 
        8.98        22.82        18.21        19.73        15.68        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NK TCGA-L5-A8NQ 
        6.28        47.93        15.48        25.12        13.55        21.37 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P 
       10.85         5.92        10.45        12.66        12.43        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25        12.62        12.46        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FU 
       12.03        13.18        13.38         0.13        12.03         5.16 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EW 
       20.38        15.35        25.81        27.09        12.43         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        18.18        52.27        18.05        11.24         9.17 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.30               0.13 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             60.39             122.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            12.850             13.165 
[1] "0.3 - 60.4 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         1        0        0        0        10         7
  17P GAIN WILD-TYPE       7        5        6        1        37        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           5          5          1          0        1
  17P GAIN WILD-TYPE        20          9          8          7        4
                    vv
clus                 STAGE IVA
  17P GAIN MUTATED           0
  17P GAIN WILD-TYPE         4
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                10                 37
  STAGE IIB                 7                 24
  STAGE III                 5                 20
  STAGE IIIA                5                  9
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  4
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  17P GAIN MUTATED       7  7 15  1
  17P GAIN WILD-TYPE    25 36 72  4
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1                7                 25
  T2                   7                 36
  T3                  15                 72
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17P GAIN MUTATED   12 16  2  0
  17P GAIN WILD-TYPE 65 52 10  8
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               12                 65
  N1               16                 52
  N2                2                 10
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    25   1
  17P GAIN WILD-TYPE 110   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     25    1
  17P GAIN WILD-TYPE  110    8
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               25                110
  1                1                  8
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     3  30
  17P GAIN WILD-TYPE  24 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3   30
  17P GAIN WILD-TYPE   24  127
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 30                127
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    18  11
  17P GAIN WILD-TYPE 106  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     18   11
  17P GAIN WILD-TYPE  106   31
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                18                106
  YES               11                 31
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   12 21
  17P GAIN WILD-TYPE 76 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     12   21
  17P GAIN WILD-TYPE   76   75
                                   clus
vv                                  17P GAIN MUTATED 17P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   12                 76
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               21                 75
[1] 2 2
[1] FALSE
D30V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    23   2   1   3
  17P GAIN WILD-TYPE 114  10   1   4
D30V12, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               23                114
  R1                2                 10
  R2                1                  1
  RX                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED      11                         1    21
  17P GAIN WILD-TYPE    35                         4    93
D30V14, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                   11                 35
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   21                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0 17
  17P GAIN WILD-TYPE  6 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   17
  17P GAIN WILD-TYPE    6   71
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               17                 71
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   28 16
  17Q GAIN WILD-TYPE 79 60
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                44                139 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 60 
$`17Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43I 
       60.39        23.18        31.56        25.22        30.25        18.28 
TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A8NE 
       24.00        18.35         3.32         1.38         4.90        55.50 
TCGA-L5-A8NG TCGA-L5-A8NN TCGA-L5-A8NT TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       35.97         5.49        27.12         7.99         7.59         5.06 
TCGA-R6-A6XG TCGA-V5-AASW TCGA-VR-AA4D TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D 
       38.40         9.27        46.19        35.21         0.53        17.03 
TCGA-IG-A625 TCGA-L5-A43H TCGA-L5-A88Z TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
       12.82         0.30         7.40        13.38        13.15        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FQ 
       12.49        12.76        12.59        12.00        13.18        12.85 
TCGA-LN-A9FR TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
       12.26         3.42        15.35         1.55        18.31        33.70 
TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.91         2.10 

$`17Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
        3.88        14.86       122.10        47.38        34.85        21.70 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        3.16         8.94        26.33         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
       21.01         7.17         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        7.43        22.82         2.60         0.36         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        83.24        52.57        46.09        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
       33.11         7.82        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ TCGA-X8-AAAR 
       20.02         5.29        16.44         8.98        22.82        18.21 
TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       19.73        15.68        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12        18.64         9.30         0.79        23.41         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S 
       41.52        24.03         6.28         4.31        47.93        15.48 
TCGA-L5-A88W TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       25.12        13.55        21.37        10.85         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49W 
       12.66        12.43        13.41        12.33        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.62        12.46        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       10.52        12.23        12.03        13.18        13.38         0.13 
TCGA-LN-A9FP TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       12.03         5.16        20.38        25.81        27.09        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
        9.17        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN 
        2.66 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.30               0.13 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             60.39             122.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             13.00              13.18 
[1] "0.3 - 60.4 (13.0)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         2        0        0        0        11         7
  17Q GAIN WILD-TYPE       6        5        6        1        36        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           7          5          3          2        2
  17Q GAIN WILD-TYPE        18          9          6          5        3
                    vv
clus                 STAGE IVA
  17Q GAIN MUTATED           0
  17Q GAIN WILD-TYPE         4
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  0                  5
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                11                 36
  STAGE IIB                 7                 24
  STAGE III                 7                 18
  STAGE IIIA                5                  9
  STAGE IIIB                3                  6
  STAGE IIIC                2                  5
  STAGE IV                  2                  3
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  17Q GAIN MUTATED       7  9 22  1
  17Q GAIN WILD-TYPE    25 34 65  4
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1                7                 25
  T2                   9                 34
  T3                  22                 65
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17Q GAIN MUTATED   15 18  4  2
  17Q GAIN WILD-TYPE 62 50  8  6
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               15                 62
  N1               18                 50
  N2                4                  8
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    32   2
  17Q GAIN WILD-TYPE 103   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     32    2
  17Q GAIN WILD-TYPE  103    7
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               32                103
  1                2                  7
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4  41
  17Q GAIN WILD-TYPE  23 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   41
  17Q GAIN WILD-TYPE   23  116
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                4                 23
  MALE                 41                116
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    23  16
  17Q GAIN WILD-TYPE 101  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23   16
  17Q GAIN WILD-TYPE  101   26
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                23                101
  YES               16                 26
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   21 24
  17Q GAIN WILD-TYPE 67 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21   24
  17Q GAIN WILD-TYPE   67   72
                                   clus
vv                                  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   21                 67
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               24                 72
[1] 2 2
[1] FALSE
D31V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    30   4   1   3
  17Q GAIN WILD-TYPE 107   8   1   4
D31V12, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               30                107
  R1                4                  8
  R2                1                  1
  RX                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED      14                         2    29
  17Q GAIN WILD-TYPE    32                         3    85
D31V14, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                   14                 32
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                   29                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V15, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0 23
  17Q GAIN WILD-TYPE  6 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   23
  17Q GAIN WILD-TYPE    6   65
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               23                 65
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   26 24
  18P GAIN WILD-TYPE 81 52
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                50                133 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                24                 52 
$`18P GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4ON 
        7.63        13.94         4.21        60.39        34.85        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NL 
        1.38         3.16         4.90         7.13         0.36        13.22 
TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-R6-A6KZ 
        5.49        13.41        27.12        83.24        46.09         5.06 
TCGA-R6-A8WG TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A97I 
       12.69        16.44        22.82         0.53        12.82        12.16 
TCGA-JY-A6FE TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A8NQ TCGA-LN-A49S TCGA-LN-A49U 
        3.68         4.31        47.93        21.37        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4MQ 
       12.59        13.25        12.62        12.76        12.59        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A9FR TCGA-S8-A6BW 
       13.22         4.47        12.33        25.25        12.26        20.38 
TCGA-V5-A7RC TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I 
        3.42        28.11        18.18        52.27        11.24        15.91 
TCGA-XP-A8T6 TCGA-Z6-A8JE 
       25.08         2.10 

$`18P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 
       16.24        32.45         7.69         3.88        14.86       122.10 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
       47.38        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25        18.28         8.94        24.00        26.33         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
       32.61        19.99        21.01         3.32         7.17        58.59 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
       29.00         7.43        22.82         2.60         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
        7.76         8.71        52.57        10.36        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.99         7.59        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         2.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR 
       20.02         5.29         9.27         8.98        46.19        18.21 
TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       19.73        15.68        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
        2.63        20.12        18.64         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD 
       23.41         9.96         4.67        14.50        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A88S TCGA-L5-A88W 
       41.52        24.03         6.28         0.30        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
        7.40        13.55        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 
       12.43        13.41        12.33        13.38        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV 
       12.49        22.39        12.85        15.52        11.54        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FU TCGA-V5-AASV TCGA-VR-A8EO 
        0.13        12.03        12.85         5.16        15.35        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       27.09        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.05         9.17        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN 
        2.66 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.36               0.13 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             83.24             122.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             12.79              13.18 
[1] "0.4 - 83.2 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         1        2        3        0         9        10
  18P GAIN WILD-TYPE       7        3        3        1        38        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED          11          4          1          1        3
  18P GAIN WILD-TYPE        14         10          8          6        2
                    vv
clus                 STAGE IVA
  18P GAIN MUTATED           1
  18P GAIN WILD-TYPE         3
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  2                  3
  STAGE IB                  3                  3
  STAGE II                  0                  1
  STAGE IIA                 9                 38
  STAGE IIB                10                 21
  STAGE III                11                 14
  STAGE IIIA                4                 10
  STAGE IIIB                1                  8
  STAGE IIIC                1                  6
  STAGE IV                  3                  2
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  18P GAIN MUTATED       8 12 26  1
  18P GAIN WILD-TYPE    24 31 61  4
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                8                 24
  T2                  12                 31
  T3                  26                 61
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18P GAIN MUTATED   20 23  2  2
  18P GAIN WILD-TYPE 57 45 10  6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               20                 57
  N1               23                 45
  N2                2                 10
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   36  4
  18P GAIN WILD-TYPE 99  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     36    4
  18P GAIN WILD-TYPE   99    5
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               36                 99
  1                4                  5
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3  47
  18P GAIN WILD-TYPE  24 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3   47
  18P GAIN WILD-TYPE   24  110
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 47                110
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   28 15
  18P GAIN WILD-TYPE 96 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     28   15
  18P GAIN WILD-TYPE   96   27
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                28                 96
  YES               15                 27
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   21 29
  18P GAIN WILD-TYPE 67 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     21   29
  18P GAIN WILD-TYPE   67   67
                                   clus
vv                                  18P GAIN MUTATED 18P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   21                 67
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               29                 67
[1] 2 2
[1] FALSE
D32V11, continuous
                    vv
clus                 R0 R1 R2 RX
  18P GAIN MUTATED   39  2  2  2
  18P GAIN WILD-TYPE 98 10  0  5
D32V12, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               39                 98
  R1                2                 10
  R2                2                  0
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED      15                         2    28
  18P GAIN WILD-TYPE    31                         3    86
D32V14, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                   15                 31
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                   28                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V15, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2 20
  18P GAIN WILD-TYPE  4 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   20
  18P GAIN WILD-TYPE    4   68
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               20                 68
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   14 12
  18Q GAIN WILD-TYPE 93 64
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                26                157 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                 64 
$`18Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-JY-A6FB TCGA-L5-A43E 
        7.63         5.92        13.94         4.21        60.39        30.25 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NL TCGA-L5-A8NN TCGA-R6-A6KZ 
        3.16         7.13         0.36        13.22         5.49         5.06 
TCGA-VR-A8EQ TCGA-IG-A3I8 TCGA-IG-A625 TCGA-JY-A6FE TCGA-L5-A8NQ TCGA-LN-A49X 
       22.82        33.27        12.82         3.68        21.37        12.62 
TCGA-LN-A4A3 TCGA-LN-A7HY TCGA-LN-A9FR TCGA-S8-A6BW TCGA-VR-A8Q7 TCGA-VR-AA7B 
       12.76        12.03        12.26        20.38        52.27        11.24 
TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.91         2.10 

$`18Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30        58.55         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH 
       32.45         7.69         3.88        14.86       122.10        47.38 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
       34.85        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       18.28         8.94        24.00        26.33         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
       58.59         4.90        29.00         7.43        22.82         2.60 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.75         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.48        16.47         7.76         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       83.24        52.57        46.09        10.36        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.99         7.59        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.02         5.29        16.44         9.27         8.98 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
       46.19        18.21        19.73        15.68        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03         0.79        23.41         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       12.16        44.75        68.02        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        0.30         4.31        47.93        15.48        25.12         7.40 
TCGA-L5-A8NK TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       13.55        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.25        12.46        12.59        12.49        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FU 
       13.38        13.18         0.13        12.03        12.85         5.16 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        3.42        15.35        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G 
       18.31         8.12        28.11        33.70        18.18        18.05 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
        9.17        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN 
        2.66 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.36               0.13 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             60.39             122.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             12.44              13.22 
[1] "0.4 - 60.4 (12.4)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         2        1        1        0         3         3
  18Q GAIN WILD-TYPE       6        4        5        1        44        28
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED          10          2          1          0        1
  18Q GAIN WILD-TYPE        15         12          8          7        4
                    vv
clus                 STAGE IVA
  18Q GAIN MUTATED           0
  18Q GAIN WILD-TYPE         4
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 3                 44
  STAGE IIB                 3                 28
  STAGE III                10                 15
  STAGE IIIA                2                 12
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  4
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  18Q GAIN MUTATED       5  4 15  1
  18Q GAIN WILD-TYPE    27 39 72  4
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                5                 27
  T2                   4                 39
  T3                  15                 72
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18Q GAIN MUTATED    9 14  1  1
  18Q GAIN WILD-TYPE 68 54 11  7
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                9                 68
  N1               14                 54
  N2                1                 11
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    21   1
  18Q GAIN WILD-TYPE 114   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     21    1
  18Q GAIN WILD-TYPE  114    8
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               21                114
  1                1                  8
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3  23
  18Q GAIN WILD-TYPE  24 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3   23
  18Q GAIN WILD-TYPE   24  134
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 23                134
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    19   4
  18Q GAIN WILD-TYPE 105  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     19    4
  18Q GAIN WILD-TYPE  105   38
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                19                105
  YES                4                 38
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED   13 13
  18Q GAIN WILD-TYPE 75 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     13   13
  18Q GAIN WILD-TYPE   75   83
                                   clus
vv                                  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   13                 75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               13                 83
[1] 2 2
[1] FALSE
D33V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    21   2   1   1
  18Q GAIN WILD-TYPE 116  10   1   6
D33V12, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               21                116
  R1                2                 10
  R2                1                  1
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       5                         0    16
  18Q GAIN WILD-TYPE    41                         5    98
D33V14, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    5                 41
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                   16                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    0  9
  18Q GAIN WILD-TYPE  6 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    9
  18Q GAIN WILD-TYPE    6   79
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO                9                 79
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   18 10
  19P GAIN WILD-TYPE 89 66
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                28                155 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                 66 
$`19P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OQ 
       58.55         8.94         3.16        24.00         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A8NG TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-R6-A6KZ TCGA-R6-A6XG 
        3.16        35.97        27.12        10.36         5.06        38.40 
TCGA-R6-A8WG TCGA-X8-AAAR TCGA-IG-A3QL TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V 
       12.69        18.21        35.21         5.92        13.15        12.59 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-S8-A6BW 
       25.25        12.00        13.18         0.13        12.85        20.38 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-AA7I 
       15.35        27.09        28.11        15.91 

$`19P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
       16.24         4.21        32.45         7.69         3.88        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OF 
       31.56        25.22        30.25        18.28         8.94        26.33 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP 
        4.70        32.61        19.99        21.01        18.35         7.17 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
       58.59         4.90        29.00         7.13         7.43        22.82 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         0.36         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 
        8.71        13.41        83.24        52.57        46.09        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.82         7.99         7.59        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         2.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
       20.02         5.29        16.44         9.27         8.98        22.82 
TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       46.19        19.73        15.68        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
        6.28         0.30         4.31        47.93        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
        7.40        13.55        21.37        10.85        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41        12.33        13.38        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-VR-A8EO 
       13.38        12.03        12.26         5.16         3.42        25.81 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 
       52.27        18.05        11.24         9.17        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       14.37         3.42         2.10         1.32         2.66 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.13               0.30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             58.55             122.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            13.165             12.920 
[1] "0.1 - 58.5 (13.2)"  "0.3 - 122.1 (12.9)"
[1] "hr=" "1.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         1        1        1        0         9         2
  19P GAIN WILD-TYPE       7        4        5        1        38        29
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           3          1          2          2        0
  19P GAIN WILD-TYPE        22         13          7          5        5
                    vv
clus                 STAGE IVA
  19P GAIN MUTATED           1
  19P GAIN WILD-TYPE         3
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 9                 38
  STAGE IIB                 2                 29
  STAGE III                 3                 22
  STAGE IIIA                1                 13
  STAGE IIIB                2                  7
  STAGE IIIC                2                  5
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  19P GAIN MUTATED       4  7 12  1
  19P GAIN WILD-TYPE    28 36 75  4
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                4                 28
  T2                   7                 36
  T3                  12                 75
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19P GAIN MUTATED   15  4  3  2
  19P GAIN WILD-TYPE 62 64  9  6
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               15                 62
  N1                4                 64
  N2                3                  9
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    16   1
  19P GAIN WILD-TYPE 119   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16    1
  19P GAIN WILD-TYPE  119    8
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               16                119
  1                1                  8
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  27
  19P GAIN WILD-TYPE  26 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   27
  19P GAIN WILD-TYPE   26  130
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                1                 26
  MALE                 27                130
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    21   6
  19P GAIN WILD-TYPE 103  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     21    6
  19P GAIN WILD-TYPE  103   36
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                21                103
  YES                6                 36
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   14 14
  19P GAIN WILD-TYPE 74 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     14   14
  19P GAIN WILD-TYPE   74   82
                                   clus
vv                                  19P GAIN MUTATED 19P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   14                 74
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               14                 82
[1] 2 2
[1] FALSE
D34V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    21   1   1   1
  19P GAIN WILD-TYPE 116  11   1   6
D34V12, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               21                116
  R1                1                 11
  R2                1                  1
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       8                         1    16
  19P GAIN WILD-TYPE    38                         4    98
D34V14, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    8                 38
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   16                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1 15
  19P GAIN WILD-TYPE  5 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   15
  19P GAIN WILD-TYPE    5   73
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               15                 73
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   21 17
  19Q GAIN WILD-TYPE 86 59
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                38                145 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                 59 
$`19Q GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A4QS TCGA-L5-A43C 
       58.55         7.63         8.94        16.24         3.88         3.16 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       24.00        26.33        32.61         3.32         1.38         3.16 
TCGA-L5-A8NG TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       35.97         5.49        27.12        52.57        46.09        10.36 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8WG TCGA-X8-AAAR TCGA-IG-A3QL 
        5.06        16.31        38.40        12.69        18.21        35.21 
TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       13.55         5.92        15.35        12.85        25.25        12.00 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EX 
        0.13        12.85        20.38        15.35        27.09        28.11 
TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.91         2.10 

$`19Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       25.78        31.27        14.30         5.92        13.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
       32.45         7.69        14.86       122.10        60.39        47.38 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E 
       34.85        21.70        23.18        31.56        25.22        30.25 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       18.28         8.94         4.70        19.99        21.01        18.35 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       22.82         2.60         0.36         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        8.71        13.41        83.24        33.11         7.82         7.99 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.59         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         2.30         7.00        20.02         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IC-A6RF 
        9.27         8.98        22.82        46.19        19.73        15.68 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L7-A56G 
       47.93        15.48        25.12         7.40        21.37        10.85 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX 
       12.33        13.22         4.47        12.33        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FR 
       12.03        13.18        13.38        13.18        12.03        12.26 
TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        5.16         3.42        25.81        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
        9.17        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN 
        2.66 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.13               0.30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             58.55             122.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             15.35              12.82 
[1] "0.1 - 58.5 (15.3)"  "0.3 - 122.1 (12.8)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         2        1        2        1         9         3
  19Q GAIN WILD-TYPE       6        4        4        0        38        28
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           5          2          3          2        0
  19Q GAIN WILD-TYPE        20         12          6          5        5
                    vv
clus                 STAGE IVA
  19Q GAIN MUTATED           2
  19Q GAIN WILD-TYPE         2
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  4
  STAGE IB                  2                  4
  STAGE II                  1                  0
  STAGE IIA                 9                 38
  STAGE IIB                 3                 28
  STAGE III                 5                 20
  STAGE IIIA                2                 12
  STAGE IIIB                3                  6
  STAGE IIIC                2                  5
  STAGE IV                  0                  5
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  19Q GAIN MUTATED       6  8 18  1
  19Q GAIN WILD-TYPE    26 35 69  4
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                6                 26
  T2                   8                 35
  T3                  18                 69
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19Q GAIN MUTATED   17 10  4  2
  19Q GAIN WILD-TYPE 60 58  8  6
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               17                 60
  N1               10                 58
  N2                4                  8
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    23   2
  19Q GAIN WILD-TYPE 112   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     23    2
  19Q GAIN WILD-TYPE  112    7
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               23                112
  1                2                  7
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  37
  19Q GAIN WILD-TYPE  26 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   37
  19Q GAIN WILD-TYPE   26  120
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                 26
  MALE                 37                120
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   32  4
  19Q GAIN WILD-TYPE 92 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     32    4
  19Q GAIN WILD-TYPE   92   38
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                32                 92
  YES                4                 38
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   23 15
  19Q GAIN WILD-TYPE 65 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     23   15
  19Q GAIN WILD-TYPE   65   81
                                   clus
vv                                  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   23                 65
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               15                 81
[1] 2 2
[1] FALSE
D35V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    26   3   1   2
  19Q GAIN WILD-TYPE 111   9   1   5
D35V12, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               26                111
  R1                3                  9
  R2                1                  1
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       7                         1    25
  19Q GAIN WILD-TYPE    39                         4    89
D35V14, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    7                 39
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   25                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1 17
  19Q GAIN WILD-TYPE  5 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   17
  19Q GAIN WILD-TYPE    5   71
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               17                 71
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   57 50
  20P GAIN WILD-TYPE 50 26
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               107                 76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                50                 26 
$`20P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A939 
        4.21        32.45         7.69         3.88       122.10        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OE 
       23.18        31.56        25.22         3.16        30.25        24.00 
TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
        4.70        18.35         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NE 
       29.00         7.13         7.43         2.60         0.36        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR 
        2.66        35.97        12.92        16.47         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-R6-A6DN 
       13.41        27.12        52.57        46.09        10.36         7.99 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06        16.31         7.04         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
       15.78         2.89        12.69        20.02         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3QL 
        9.27         8.98        46.19        19.73        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        0.85         2.63        20.12         0.53        17.03        23.41 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FE TCGA-L5-A43H TCGA-L5-A43J 
        4.67        14.50        12.16         3.68         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88Z TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49P 
       47.93        15.48         7.40        10.85        10.45        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.38        13.15        12.62        12.49        12.76        12.85 
TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I1 
       11.54        12.33        25.25        12.23        13.18        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW 
        0.13        12.85         3.42        27.09         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        33.70        18.18        52.27        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       15.91        25.08         2.10         1.32         2.66 

$`20P GAIN WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH 
       14.30        58.55         7.63        14.86        60.39        47.38 
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
       34.85        18.28         8.94        26.33        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A88T TCGA-L5-A891 TCGA-L5-A893 
       21.01         3.32         3.16        22.82         3.75         3.02 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NU TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.48        13.22         7.76        83.24        33.11         7.82 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-VR-A8EQ TCGA-X8-AAAR 
       38.40        53.95         2.30         7.00        22.82        18.21 
TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 
       15.68        20.78        18.64         9.30         0.79        12.82 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
        9.96        44.75        68.02        41.52        24.03         6.28 
TCGA-L5-A88W TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       25.12        13.55        21.37         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       13.41        15.35        12.59        13.25        12.46        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        22.39        15.52        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR 
       10.52        12.00        12.03        13.38        12.03        12.26 
TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU 
        5.16        20.38        15.35        25.81        12.43        18.31 
TCGA-VR-AA4G TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05        41.23        14.37         3.42 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.13               0.79 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            122.10              83.24 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            12.620             13.515 
[1] "0.1 - 122.1 (12.6)" "0.8 - 83.2 (13.5)" 
[1] "hr=" "1.6"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         3        2        3        1        24        17
  20P GAIN WILD-TYPE       5        3        3        0        23        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED          14         10          6          5        3
  20P GAIN WILD-TYPE        11          4          3          2        2
                    vv
clus                 STAGE IVA
  20P GAIN MUTATED           4
  20P GAIN WILD-TYPE         0
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  2                  3
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                24                 23
  STAGE IIB                17                 14
  STAGE III                14                 11
  STAGE IIIA               10                  4
  STAGE IIIB                6                  3
  STAGE IIIC                5                  2
  STAGE IV                  3                  2
  STAGE IVA                 4                  0
[1] 12  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                 T0+T1 T2 T3 T4
  20P GAIN MUTATED      19 21 52  2
  20P GAIN WILD-TYPE    13 22 35  3
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               19                 13
  T2                  21                 22
  T3                  52                 35
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20P GAIN MUTATED   39 41  7  6
  20P GAIN WILD-TYPE 38 27  5  2
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               39                 38
  N1               41                 27
  N2                7                  5
  N3                6                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   74  7
  20P GAIN WILD-TYPE 61  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     74    7
  20P GAIN WILD-TYPE   61    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               74                 61
  1                7                  2
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   13 95
  20P GAIN WILD-TYPE 14 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     13   95
  20P GAIN WILD-TYPE   14   62
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               13                 14
  MALE                 95                 62
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   75 22
  20P GAIN WILD-TYPE 49 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     75   22
  20P GAIN WILD-TYPE   49   20
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                75                 49
  YES               22                 20
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   58 50
  20P GAIN WILD-TYPE 30 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     58   50
  20P GAIN WILD-TYPE   30   46
                                   clus
vv                                  20P GAIN MUTATED 20P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   58                 30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               50                 46
[1] 2 2
[1] FALSE
D36V11, continuous
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   78  8  1  4
  20P GAIN WILD-TYPE 59  4  1  3
D36V12, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               78                 59
  R1                8                  4
  R2                1                  1
  RX                4                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED      22                         3    70
  20P GAIN WILD-TYPE    24                         2    44
D36V14, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                   22                 24
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   70                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    4 49
  20P GAIN WILD-TYPE  2 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4   49
  20P GAIN WILD-TYPE    2   39
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               49                 39
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   60 54
  20Q GAIN WILD-TYPE 47 22
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               114                 69 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                54                 22 
$`20Q GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        8.94        16.24         4.21        32.45         7.69         3.88 
TCGA-JY-A6F8 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
      122.10        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4ON 
       30.25        24.00        26.33         4.70        32.61        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NF 
        7.13         7.43         2.60         0.36        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR 
       35.97        12.92        16.47        13.22         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-R6-A6DN 
       13.41        27.12        52.57        46.09        10.36         7.99 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4D 
       20.02         5.29        16.44         9.27         8.98        46.19 
TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A50L 
       19.73        33.27         0.85         2.63        20.12         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FE 
       17.03        23.41         4.67        14.50        12.16         3.68 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A8NQ 
        0.30         4.31        47.93        15.48         7.40        21.37 
TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
       10.85        10.45        12.33        13.38        13.15        12.59 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.62        12.49        12.76        12.85        12.33        25.25 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       12.23        12.03        13.18        13.18         0.13        12.85 
TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
        3.42        27.09         1.55         8.12        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-AAPN 
       52.27        11.24         9.17        25.08         2.10         2.66 

$`20Q GAIN WILD-TYPE`
TCGA-2H-A9GL TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-L5-A43I 
        5.92        14.86        60.39        47.38        34.85        18.28 
TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A88T TCGA-L5-A891 
        8.94        19.99        21.01         3.32        22.82         3.75 
TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NU TCGA-M9-A5M8 TCGA-Q9-A6FW 
        3.02        13.48         7.76        83.24        33.11         7.82 
TCGA-R6-A8WC TCGA-VR-A8EQ TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA 
        2.30        22.82        18.21        15.68        35.21        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-JY-A6FA 
       18.64         9.30         0.79        12.82         9.96        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A88W TCGA-L5-A8NK 
       68.02        41.52        24.03         6.28        25.12        13.55 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W 
        5.92        12.66        12.43        13.41        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.59        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A8I0 
       12.33        13.22         4.47        10.52        12.00        13.38 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO 
       12.03        12.26         5.16        20.38        15.35        25.81 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I TCGA-XP-A8T7 
       12.43        18.31        33.70        18.05        15.91        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       14.37         3.42         1.32 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.13               0.79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            122.10              83.24 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            12.725             13.480 
[1] "0.1 - 122.1 (12.7)" "0.8 - 83.2 (13.5)" 
[1] "hr=" "1.6"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         5        3        3        1        23        19
  20Q GAIN WILD-TYPE       3        2        3        0        24        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED          16          9          6          5        3
  20Q GAIN WILD-TYPE         9          5          3          2        2
                    vv
clus                 STAGE IVA
  20Q GAIN MUTATED           4
  20Q GAIN WILD-TYPE         0
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   5                  3
  STAGE IA                  3                  2
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                23                 24
  STAGE IIB                19                 12
  STAGE III                16                  9
  STAGE IIIA                9                  5
  STAGE IIIB                6                  3
  STAGE IIIC                5                  2
  STAGE IV                  3                  2
  STAGE IVA                 4                  0
[1] 12  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                 T0+T1 T2 T3 T4
  20Q GAIN MUTATED      24 20 54  1
  20Q GAIN WILD-TYPE     8 23 33  4
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               24                  8
  T2                  20                 23
  T3                  54                 33
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   40 45  7  6
  20Q GAIN WILD-TYPE 37 23  5  2
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               40                 37
  N1               45                 23
  N2                7                  5
  N3                6                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   77  7
  20Q GAIN WILD-TYPE 58  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     77    7
  20Q GAIN WILD-TYPE   58    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               77                 58
  1                7                  2
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    13 102
  20Q GAIN WILD-TYPE  14  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     13  102
  20Q GAIN WILD-TYPE   14   55
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               13                 14
  MALE                102                 55
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   80 23
  20Q GAIN WILD-TYPE 44 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     80   23
  20Q GAIN WILD-TYPE   44   19
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                80                 44
  YES               23                 19
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   67 48
  20Q GAIN WILD-TYPE 21 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     67   48
  20Q GAIN WILD-TYPE   21   48
                                   clus
vv                                  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   67                 21
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               48                 48
[1] 2 2
[1] FALSE
D37V11, continuous
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED   84  7  0  4
  20Q GAIN WILD-TYPE 53  5  2  3
D37V12, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               84                 53
  R1                7                  5
  R2                0                  2
  RX                4                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED      23                         3    74
  20Q GAIN WILD-TYPE    23                         2    40
D37V14, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                   23                 23
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   74                 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"
D37V15, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    4 51
  20Q GAIN WILD-TYPE  2 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4   51
  20Q GAIN WILD-TYPE    2   37
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               51                 37
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   13  5
  21Q GAIN WILD-TYPE 94 71
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                18                165 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 71 
$`21Q GAIN MUTATED`
TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A8NE TCGA-L5-A8NN TCGA-S8-A6BV TCGA-X8-AAAR 
       25.22        26.33        55.50         5.49        20.02        18.21 
TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-LN-A49L TCGA-LN-A49U 
        2.63        23.41         4.67        14.50        10.45        15.35 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A8I1 TCGA-V5-A7RC TCGA-VR-A8EP TCGA-XP-A8T6 
       12.59        12.59        13.18         3.42        27.09        25.08 

$`21Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 
        3.88        14.86       122.10        60.39        47.38        34.85 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I 
       21.70        23.18        31.56         3.16        30.25        18.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94        24.00         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        22.82         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         3.75         3.02         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        16.47        13.22         7.76         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       27.12        83.24        52.57        46.09        10.36        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         7.99         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        2.30        12.69         7.00         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 
        8.98        22.82        46.19        19.73        15.68        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       35.21         0.85        20.78        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97I 
        0.53        17.03         0.79        12.82         9.96        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        0.30         4.31        47.93        15.48        25.12         7.40 
TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       13.55        21.37        10.85         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X 
       13.41        12.33        13.38        13.15        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU 
       13.38         0.13        12.03        12.85        12.26         5.16 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       20.38        15.35        25.81        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       11.24         9.17        15.91        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        2.10         1.32         2.66 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2.63               0.13 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              55.5              122.1 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            14.925             12.850 
[1] "2.6 - 55.5 (14.9)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.6"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         0        0        0        0         6         4
  21Q GAIN WILD-TYPE       8        5        6        1        41        27
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           1          3          2          0        0
  21Q GAIN WILD-TYPE        24         11          7          7        5
                    vv
clus                 STAGE IVA
  21Q GAIN MUTATED           0
  21Q GAIN WILD-TYPE         4
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 6                 41
  STAGE IIB                 4                 27
  STAGE III                 1                 24
  STAGE IIIA                3                 11
  STAGE IIIB                2                  7
  STAGE IIIC                0                  7
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  21Q GAIN MUTATED       2  4 11  0
  21Q GAIN WILD-TYPE    30 39 76  5
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                2                 30
  T2                   4                 39
  T3                  11                 76
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  21Q GAIN MUTATED    6  8  2  0
  21Q GAIN WILD-TYPE 71 60 10  8
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                6                 71
  N1                8                 60
  N2                2                 10
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    14   0
  21Q GAIN WILD-TYPE 121   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     14    0
  21Q GAIN WILD-TYPE  121    9
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               14                121
  1                0                  9
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2  16
  21Q GAIN WILD-TYPE  25 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2   16
  21Q GAIN WILD-TYPE   25  141
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                 16                141
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    10   6
  21Q GAIN WILD-TYPE 114  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    6
  21Q GAIN WILD-TYPE  114   36
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                10                114
  YES                6                 36
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    6 12
  21Q GAIN WILD-TYPE 82 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6   12
  21Q GAIN WILD-TYPE   82   84
                                   clus
vv                                  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                    6                 82
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               12                 84
[1] 2 2
[1] FALSE
D38V11, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    13   0   0   0
  21Q GAIN WILD-TYPE 124  12   2   7
D38V12, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               13                124
  R1                0                 12
  R2                0                  2
  RX                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       7                         2     9
  21Q GAIN WILD-TYPE    39                         3   105
D38V14, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    7                 39
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                    9                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    1 12
  21Q GAIN WILD-TYPE  5 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   12
  21Q GAIN WILD-TYPE    5   76
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               12                 76
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   20 10
  22Q GAIN WILD-TYPE 87 66
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                30                153 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                 66 
$`22Q GAIN MUTATED`
TCGA-L5-A43E TCGA-L5-A8NT TCGA-R6-A8WG TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       30.25        27.12        12.69        35.21         0.85        20.78 
TCGA-IG-A97H TCGA-L5-A43J TCGA-L5-A4OM TCGA-LN-A49P TCGA-LN-A4A1 TCGA-LN-A4A2 
       14.50         4.31        47.93        12.33        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.59        12.85        11.54        12.33        13.22        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-Q9-A6FU TCGA-S8-A6BW 
       12.00        12.23         0.13        12.85         5.16        20.38 
TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B 
        3.42        27.09         8.12        28.11        18.18        11.24 

$`22Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 
        3.88        14.86       122.10        60.39        47.38        34.85 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I 
       21.70        23.18        31.56        25.22         3.16        18.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00        26.33         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
       58.59         4.90        29.00         7.13         7.43        22.82 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         0.36         3.75         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       10.36        33.11         7.82         7.99         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR 
       16.44         9.27         8.98        22.82        46.19        18.21 
TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       19.73        15.68        33.27         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        9.96         4.67        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A88S TCGA-L5-A88W 
       41.52        24.03         6.28         0.30        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
        7.40        13.55        21.37        10.85         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 
       12.59        13.25        12.62        12.46        12.76        22.39 
TCGA-LN-A4A8 TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ 
       15.52         4.47        25.25        10.52        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-V5-AASV TCGA-VR-A8EO 
       13.38        13.18        12.03        12.26        15.35        25.81 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G 
       12.43         1.55        18.31        33.70        52.27        18.05 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        2.10         1.32         2.66 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.13               0.30 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             47.93             122.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             12.59              13.25 
[1] "0.1 - 47.9 (12.6)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1        1        1        1        12         3
  22Q GAIN WILD-TYPE       7        4        5        0        35        28
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           2          2          3          1        1
  22Q GAIN WILD-TYPE        23         12          6          6        4
                    vv
clus                 STAGE IVA
  22Q GAIN MUTATED           1
  22Q GAIN WILD-TYPE         3
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                12                 35
  STAGE IIB                 3                 28
  STAGE III                 2                 23
  STAGE IIIA                2                 12
  STAGE IIIB                3                  6
  STAGE IIIC                1                  6
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  22Q GAIN MUTATED       3 10 14  2
  22Q GAIN WILD-TYPE    29 33 73  3
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1                3                 29
  T2                  10                 33
  T3                  14                 73
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  22Q GAIN MUTATED   19  4  3  2
  22Q GAIN WILD-TYPE 58 64  9  6
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               19                 58
  N1                4                 64
  N2                3                  9
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    24   2
  22Q GAIN WILD-TYPE 111   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     24    2
  22Q GAIN WILD-TYPE  111    7
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               24                111
  1                2                  7
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  28
  22Q GAIN WILD-TYPE  24 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   28
  22Q GAIN WILD-TYPE   24  129
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 28                129
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    22   7
  22Q GAIN WILD-TYPE 102  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     22    7
  22Q GAIN WILD-TYPE  102   35
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                22                102
  YES                7                 35
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    3 28
  22Q GAIN WILD-TYPE 85 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   28
  22Q GAIN WILD-TYPE   85   68
                                   clus
vv                                  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                    3                 85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               28                 68
[1] 2 2
[1] FALSE
D39V11, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    24   1   0   2
  22Q GAIN WILD-TYPE 113  11   2   5
D39V12, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               24                113
  R1                1                 11
  R2                0                  2
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED      16                         1    13
  22Q GAIN WILD-TYPE    30                         4   101
D39V14, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                   16                 30
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   13                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    1 21
  22Q GAIN WILD-TYPE  5 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   21
  22Q GAIN WILD-TYPE    5   67
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               21                 67
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED   14  9
  XP GAIN WILD-TYPE 93 67
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               23               160 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                9                67 
$`XP GAIN MUTATED`
TCGA-JY-A6F8 TCGA-L5-A4OI TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A8NN 
      122.10        19.99         1.38         3.16         0.36         5.49 
TCGA-R6-A8W8 TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IG-A51D TCGA-L5-A43J TCGA-L5-A8NQ 
        2.89        46.19        19.73        17.03         4.31        21.37 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A7HZ TCGA-LN-A8I1 
       13.15        12.59        12.49        12.59        13.18        13.18 
TCGA-LN-A9FQ TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.85         3.42        15.35        33.70        18.18 

$`XP GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
        3.88        14.86        60.39        47.38        34.85        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I 
       23.18        31.56        25.22         3.16        30.25        18.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        8.94        24.00        26.33         4.70        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         7.17        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
        7.13         7.43        22.82         2.60         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22         7.76         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       52.57        46.09        10.36        33.11         7.82         7.99 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30        15.78         2.30        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
       20.02         5.29        16.44         9.27         8.98        22.82 
TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       18.21        15.68        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
        2.63        20.12        18.64         9.30         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK 
        0.30        47.93        15.48        25.12         7.40        13.55 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.33        13.38        15.35        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.76        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        12.23        12.03        13.38         0.13        12.03 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       12.26         5.16        20.38        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G 
        1.55        18.31         8.12        28.11        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        3.42         2.10         1.32         2.66 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.36              0.13 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           122.10             83.24 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            13.15             13.07 
[1] "0.4 - 122.1 (13.2)" "0.1 - 83.2 (13.1)" 
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         1        1        0        0         8         4
  XP GAIN WILD-TYPE       7        4        6        1        39        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           2          1          0          3        0
  XP GAIN WILD-TYPE        23         13          9          4        5
                   vv
clus                STAGE IVA
  XP GAIN MUTATED           0
  XP GAIN WILD-TYPE         4
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 1                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                8                39
  STAGE IIB                4                27
  STAGE III                2                23
  STAGE IIIA               1                13
  STAGE IIIB               0                 9
  STAGE IIIC               3                 4
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  XP GAIN MUTATED       5  4 12  0
  XP GAIN WILD-TYPE    27 39 75  5
D40V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1               5                27
  T2                  4                39
  T3                 12                75
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  XP GAIN MUTATED   13  4  1  3
  XP GAIN WILD-TYPE 64 64 11  5
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              13                64
  N1               4                64
  N2               1                11
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    14   0
  XP GAIN WILD-TYPE 121   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     14    0
  XP GAIN WILD-TYPE  121    9
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              14               121
  1               0                 9
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     2  21
  XP GAIN WILD-TYPE  25 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2   21
  XP GAIN WILD-TYPE   25  136
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               2                25
  MALE                21               136
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    13   8
  XP GAIN WILD-TYPE 111  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     13    8
  XP GAIN WILD-TYPE  111   34
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               13               111
  YES               8                34
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    9 14
  XP GAIN WILD-TYPE 79 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      9   14
  XP GAIN WILD-TYPE   79   82
                                   clus
vv                                  XP GAIN MUTATED XP GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   9                79
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              14                82
[1] 2 2
[1] FALSE
D40V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    17   0   0   2
  XP GAIN WILD-TYPE 120  12   2   5
D40V12, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              17               120
  R1               0                12
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       7                         2    14
  XP GAIN WILD-TYPE    39                         3   100
D40V14, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   7                39
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  14               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    0 12
  XP GAIN WILD-TYPE  6 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   12
  XP GAIN WILD-TYPE    6   76
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              12                76
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   23 15
  XQ GAIN WILD-TYPE 84 61
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               38               145 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               15                61 
$`XQ GAIN MUTATED`
TCGA-2H-A9GI TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A93C TCGA-L5-A4OI TCGA-L5-A4OQ 
       14.30         3.88       122.10        23.18        19.99         1.38 
TCGA-L5-A88Y TCGA-L5-A8NN TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-VR-AA4D TCGA-ZR-A9CJ 
        0.36         5.49         2.89        20.02        46.19        19.73 
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
       35.21         0.53        17.03        23.41         9.96         4.67 
TCGA-JY-A6FA TCGA-L5-A43J TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49V 
       44.75         4.31        21.37         5.92        12.66        12.59 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A7HZ TCGA-LN-A8I1 
       12.62        12.59        12.49        12.59        13.18        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       12.85        12.26        15.35        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-XP-A8T8 
       18.18        14.37 

$`XQ GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A7DP 
        8.94        16.24         4.21        32.45         7.69        14.86 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       60.39        47.38        34.85        21.70        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16        30.25        18.28         8.94        24.00        26.33 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        4.70        32.61        21.01        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       22.82         2.60         3.75         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       10.36        33.11         7.82         7.99         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
       15.78         2.30        12.69         7.00         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3I8 
        9.27         8.98        22.82        18.21        15.68        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE 
        0.79        12.82        14.50        12.16        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88S 
       41.52        24.03         6.28         0.30        47.93        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49N 
       25.12         7.40        13.55        10.85        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.76        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        12.23        12.03        13.38         0.13        12.03 
TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
        5.16        20.38         3.42        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
        1.55        28.11        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        25.08        41.23         3.42         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.36              0.13 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           122.10             83.24 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           13.015            13.150 
[1] "0.4 - 122.1 (13.0)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         1        0        0        0        12         9
  XQ GAIN WILD-TYPE       7        5        6        1        35        22
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           3          3          4          3        1
  XQ GAIN WILD-TYPE        22         11          5          4        4
                   vv
clus                STAGE IVA
  XQ GAIN MUTATED           0
  XQ GAIN WILD-TYPE         4
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA               12                35
  STAGE IIB                9                22
  STAGE III                3                22
  STAGE IIIA               3                11
  STAGE IIIB               4                 5
  STAGE IIIC               3                 4
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  XQ GAIN MUTATED       6  9 22  0
  XQ GAIN WILD-TYPE    26 34 65  5
D41V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               6                26
  T2                  9                34
  T3                 22                65
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  XQ GAIN MUTATED   17 12  5  3
  XQ GAIN WILD-TYPE 60 56  7  5
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              17                60
  N1              12                56
  N2               5                 7
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    29   1
  XQ GAIN WILD-TYPE 106   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     29    1
  XQ GAIN WILD-TYPE  106    8
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              29               106
  1               1                 8
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3  35
  XQ GAIN WILD-TYPE  24 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   35
  XQ GAIN WILD-TYPE   24  122
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               3                24
  MALE                35               122
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    23  11
  XQ GAIN WILD-TYPE 101  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     23   11
  XQ GAIN WILD-TYPE  101   31
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               23               101
  YES              11                31
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   12 26
  XQ GAIN WILD-TYPE 76 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12   26
  XQ GAIN WILD-TYPE   76   70
                                   clus
vv                                  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  12                76
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              26                70
[1] 2 2
[1] FALSE
D41V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    31   0   0   2
  XQ GAIN WILD-TYPE 106  12   2   5
D41V12, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              31               106
  R1               0                12
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED      16                         2    19
  XQ GAIN WILD-TYPE    30                         3    95
D41V14, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                  16                30
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  19                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    1 22
  XQ GAIN WILD-TYPE  5 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   22
  XQ GAIN WILD-TYPE    5   66
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              22                66
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   22 15
  1P LOSS WILD-TYPE 85 61
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               37               146 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15                61 
$`1P LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR TCGA-JY-A6FB TCGA-JY-A93C 
       14.30         7.63        16.24        32.45        60.39        23.18 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88V 
        8.94        24.00         4.70         4.90        29.00         2.60 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-R6-A6DN TCGA-R6-A6DQ 
       55.50        35.97        12.92        16.47         7.99         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-A7RE TCGA-V5-AASW 
        5.06         6.35         2.89         2.30        16.44         9.27 
TCGA-V5-AASX TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-L5-A43H TCGA-L5-A88Z TCGA-LN-A5U7 
        8.98        33.27        18.64         0.30         7.40        25.25 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FQ TCGA-S8-A6BW TCGA-VR-A8ER TCGA-XP-A8T8 
       12.00        13.18        12.85        20.38        12.43        14.37 
TCGA-Z6-A9VB 
        1.32 

$`1P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH 
        4.21         7.69         3.88        14.86       122.10        47.38 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       34.85        21.70        31.56        25.22         3.16        30.25 
TCGA-L5-A43I TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       18.28        26.33        32.61        19.99        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        3.32         7.17         1.38         3.16        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        7.43        22.82         0.36         3.75         3.02         2.66 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       27.12        83.24        52.57        46.09        10.36        33.11 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.82        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-VR-A8EQ 
       15.78        12.69         7.00        20.02         5.29        22.82 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
       46.19        18.21        19.73        15.68        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63        20.12         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NK 
        6.28         4.31        47.93        15.48        25.12        13.55 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        12.33        10.52        12.23        12.03 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU 
       13.38        13.18         0.13        12.03        12.26         5.16 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU 
        3.42        15.35        25.81        27.09         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
       11.24         9.17        15.91        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN 
        2.10         2.66 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.30              0.13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            60.39            122.10 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            12.85             13.20 
[1] "0.3 - 60.4 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         2        0        2        0         9         3
  1P LOSS WILD-TYPE       6        5        4        1        38        28
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           7          1          2          0        2
  1P LOSS WILD-TYPE        18         13          7          7        3
                   vv
clus                STAGE IVA
  1P LOSS MUTATED           1
  1P LOSS WILD-TYPE         3
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 0                 5
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA                9                38
  STAGE IIB                3                28
  STAGE III                7                18
  STAGE IIIA               1                13
  STAGE IIIB               2                 7
  STAGE IIIC               0                 7
  STAGE IV                 2                 3
  STAGE IVA                1                 3
[1] 12  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                T0+T1 T2 T3 T4
  1P LOSS MUTATED       6  7 16  1
  1P LOSS WILD-TYPE    26 36 71  4
D42V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               6                26
  T2                  7                36
  T3                 16                71
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  1P LOSS MUTATED   13 14  3  0
  1P LOSS WILD-TYPE 64 54  9  8
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              13                64
  N1              14                54
  N2               3                 9
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    23   3
  1P LOSS WILD-TYPE 112   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     23    3
  1P LOSS WILD-TYPE  112    6
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              23               112
  1               3                 6
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     5  33
  1P LOSS WILD-TYPE  22 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   33
  1P LOSS WILD-TYPE   22  124
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               5                22
  MALE                33               124
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   28  5
  1P LOSS WILD-TYPE 96 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     28    5
  1P LOSS WILD-TYPE   96   37
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               28                96
  YES               5                37
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   25 13
  1P LOSS WILD-TYPE 63 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     25   13
  1P LOSS WILD-TYPE   63   83
                                   clus
vv                                  1P LOSS MUTATED 1P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  25                63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              13                83
[1] 2 2
[1] FALSE
D42V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    22   6   0   2
  1P LOSS WILD-TYPE 115   6   2   5
D42V12, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              22               115
  R1               6                 6
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       6                         1    25
  1P LOSS WILD-TYPE    40                         4    89
D42V14, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   6                40
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  25                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1 18
  1P LOSS WILD-TYPE  5 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   18
  1P LOSS WILD-TYPE    5   70
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              18                70
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   10 11
  1Q LOSS WILD-TYPE 97 65
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21               162 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               11                65 
$`1Q LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A4QS TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OT 
        7.63        16.24         3.88         8.94        24.00         4.90 
TCGA-L5-A88V TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 
        2.60         7.99         7.59         5.06         6.35         2.89 
TCGA-R6-A8WC TCGA-V5-A7RE TCGA-V5-AASX TCGA-IG-A3I8 TCGA-LN-A49O TCGA-LN-A5U7 
        2.30        16.44         8.98        33.27        13.41        25.25 
TCGA-S8-A6BW TCGA-VR-A8ER TCGA-XP-A8T8 
       20.38        12.43        14.37 

$`1Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6F8 
        8.94         4.21        32.45         7.69        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       60.39        47.38        34.85        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OF TCGA-L5-A4OG 
       25.22         3.16        30.25        18.28        26.33         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       22.82         0.36         3.75         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 
       46.09        10.36        33.11         7.82        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO 
       38.40        53.95         9.30        15.78        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR 
       20.02         5.29         9.27        22.82        46.19        18.21 
TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       19.73        15.68        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        0.30         4.31        47.93        15.48        25.12         7.40 
TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       13.55        21.37        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO 
       12.85        12.26         5.16         3.42        15.35        25.81 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       27.09         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23         3.42         2.10         1.32         2.66 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2.30              0.13 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            33.27            122.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             8.94             13.20 
[1] "2.3 - 33.3 (8.9)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "2.1"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        0        2        0         4         1
  1Q LOSS WILD-TYPE       8        5        4        1        43        30
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           3          0          2          0        1
  1Q LOSS WILD-TYPE        22         14          7          7        4
                   vv
clus                STAGE IVA
  1Q LOSS MUTATED           1
  1Q LOSS WILD-TYPE         3
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 5
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA                4                43
  STAGE IIB                1                30
  STAGE III                3                22
  STAGE IIIA               0                14
  STAGE IIIB               2                 7
  STAGE IIIC               0                 7
  STAGE IV                 1                 4
  STAGE IVA                1                 3
[1] 12  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                T0+T1 T2 T3 T4
  1Q LOSS MUTATED       2  3  9  1
  1Q LOSS WILD-TYPE    30 40 78  4
D43V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               2                30
  T2                  3                40
  T3                  9                78
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  1Q LOSS MUTATED    6  6  3  0
  1Q LOSS WILD-TYPE 71 62  9  8
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               6                71
  N1               6                62
  N2               3                 9
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9   2
  1Q LOSS WILD-TYPE 126   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9    2
  1Q LOSS WILD-TYPE  126    7
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               9               126
  1               2                 7
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  19
  1Q LOSS WILD-TYPE  24 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   19
  1Q LOSS WILD-TYPE   24  138
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                19               138
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    14   4
  1Q LOSS WILD-TYPE 110  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14    4
  1Q LOSS WILD-TYPE  110   38
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               14               110
  YES               4                38
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   15  7
  1Q LOSS WILD-TYPE 73 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     15    7
  1Q LOSS WILD-TYPE   73   89
                                   clus
vv                                  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  15                73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               7                89
[1] 2 2
[1] FALSE
D43V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     9   4   0   2
  1Q LOSS WILD-TYPE 128   8   2   5
D43V12, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               9               128
  R1               4                 8
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       3                         1    14
  1Q LOSS WILD-TYPE    43                         4   100
D43V14, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   3                43
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  14               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    1 14
  1Q LOSS WILD-TYPE  5 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   14
  1Q LOSS WILD-TYPE    5   74
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              14                74
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED   10  1
  2P LOSS WILD-TYPE 97 75
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               172 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                75 
$`2P LOSS MUTATED`
TCGA-L5-A4OS TCGA-L5-A8NE TCGA-R6-A8W8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-L5-A8NK 
       58.59        55.50         2.89         2.63        20.12        13.55 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-AAPN 
       10.52        12.23        25.81        52.27         2.66 

$`2P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 
        3.88        14.86       122.10        60.39        47.38        34.85 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        31.56        25.22         3.16        30.25 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       18.28         8.94        24.00        26.33         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        3.16         4.90        29.00         7.13         7.43        22.82 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         0.36         3.75         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       10.36        33.11         7.82         7.99         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.30        12.69         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR 
       16.44         9.27         8.98        22.82        46.19        18.21 
TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       19.73        15.68        33.27        35.21         0.85        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H 
       68.02         3.68        41.52        24.03         6.28         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ 
        4.31        47.93        15.48        25.12         7.40        21.37 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        25.25        12.00        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER 
        5.16        20.38         3.42        15.35        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       14.37         3.42         2.10         1.32 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.63              0.13 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            58.59            122.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           13.550            13.035 
[1] "2.6 - 58.6 (13.6)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "6.8"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        0        0         5         2
  2P LOSS WILD-TYPE       8        5        6        1        42        29
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           0          3          0          0        0
  2P LOSS WILD-TYPE        25         11          9          7        5
                   vv
clus                STAGE IVA
  2P LOSS MUTATED           0
  2P LOSS WILD-TYPE         4
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                5                42
  STAGE IIB                2                29
  STAGE III                0                25
  STAGE IIIA               3                11
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  2P LOSS MUTATED       0  4  6  0
  2P LOSS WILD-TYPE    32 39 81  5
D44V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               0                32
  T2                  4                39
  T3                  6                81
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  2P LOSS MUTATED    5  5  0  0
  2P LOSS WILD-TYPE 72 63 12  8
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               5                72
  N1               5                63
  N2               0                12
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    10   0
  2P LOSS WILD-TYPE 125   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10    0
  2P LOSS WILD-TYPE  125    9
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              10               125
  1               0                 9
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2   9
  2P LOSS WILD-TYPE  25 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    9
  2P LOSS WILD-TYPE   25  148
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                25
  MALE                 9               148
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     6   4
  2P LOSS WILD-TYPE 118  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    4
  2P LOSS WILD-TYPE  118   38
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                6               118
  YES               4                38
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    3  8
  2P LOSS WILD-TYPE 85 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    8
  2P LOSS WILD-TYPE   85   88
                                   clus
vv                                  2P LOSS MUTATED 2P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   3                85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               8                88
[1] 2 2
[1] FALSE
D44V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     9   1   0   0
  2P LOSS WILD-TYPE 128  11   2   7
D44V12, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               9               128
  R1               1                11
  R2               0                 2
  RX               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       2                         0     9
  2P LOSS WILD-TYPE    44                         5   105
D44V14, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   2                44
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   9               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    0  6
  2P LOSS WILD-TYPE  6 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    6
  2P LOSS WILD-TYPE    6   82
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               6                82
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED   13  5
  2Q LOSS WILD-TYPE 94 71
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               165 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                71 
$`2Q LOSS MUTATED`
TCGA-L5-A4OS TCGA-L5-A893 TCGA-L5-A8NJ TCGA-R6-A8W8 TCGA-IG-A3YB TCGA-IG-A3YC 
       58.59         3.02        16.47         2.89         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A43H TCGA-L5-A8NK TCGA-LN-A49L TCGA-LN-A49Y 
       18.64         0.79         0.30        13.55        10.45        12.46 
TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HX TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-AAPN 
       12.33        10.52        12.23        25.81        52.27         2.66 

$`2Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 
        3.88        14.86       122.10        60.39        47.38        34.85 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        31.56        25.22         3.16        30.25 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       18.28         8.94        24.00        26.33         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        3.16         4.90        29.00         7.13         7.43        22.82 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         0.36         3.75        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       12.92        13.48        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         7.99         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.02         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ 
        9.27         8.98        22.82        46.19        18.21        19.73 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT 
       15.68        33.27        35.21         0.85        20.78         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.53        17.03        23.41        12.82         9.96         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
       24.03         6.28         4.31        47.93        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
        7.40        21.37        10.85         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       12.33        25.25        12.00        12.03        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU 
       13.18         0.13        12.03        12.85        12.26         5.16 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
       20.38         3.42        15.35        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G 
       18.31         8.12        28.11        33.70        18.18        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
        3.42         2.10         1.32 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.30              0.13 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            58.59            122.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            12.28             13.18 
[1] "0.3 - 58.6 (12.3)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         1        0        1        0         7         2
  2Q LOSS WILD-TYPE       7        5        5        1        40        29
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           3          3          0          0        0
  2Q LOSS WILD-TYPE        22         11          9          7        5
                   vv
clus                STAGE IVA
  2Q LOSS MUTATED           0
  2Q LOSS WILD-TYPE         4
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                7                40
  STAGE IIB                2                29
  STAGE III                3                22
  STAGE IIIA               3                11
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  2Q LOSS MUTATED       1  5 11  0
  2Q LOSS WILD-TYPE    31 38 76  5
D45V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               1                31
  T2                  5                38
  T3                 11                76
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  2Q LOSS MUTATED    9  8  0  0
  2Q LOSS WILD-TYPE 68 60 12  8
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               9                68
  N1               8                60
  N2               0                12
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    17   0
  2Q LOSS WILD-TYPE 118   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17    0
  2Q LOSS WILD-TYPE  118    9
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              17               118
  1               0                 9
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     3  15
  2Q LOSS WILD-TYPE  24 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   15
  2Q LOSS WILD-TYPE   24  142
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                15               142
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11   6
  2Q LOSS WILD-TYPE 113  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11    6
  2Q LOSS WILD-TYPE  113   36
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               11               113
  YES               6                36
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    4 14
  2Q LOSS WILD-TYPE 84 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4   14
  2Q LOSS WILD-TYPE   84   82
                                   clus
vv                                  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   4                84
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              14                82
[1] 2 2
[1] FALSE
D45V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    15   2   0   0
  2Q LOSS WILD-TYPE 122  10   2   7
D45V12, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              15               122
  R1               2                10
  R2               0                 2
  RX               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       5                         0    13
  2Q LOSS WILD-TYPE    41                         5   101
D45V14, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   5                41
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  13               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    0 11
  2Q LOSS WILD-TYPE  6 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   11
  2Q LOSS WILD-TYPE    6   77
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              11                77
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   66 26
  3P LOSS WILD-TYPE 41 50
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               92                91 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               26                50 
$`3P LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-JY-A938 TCGA-L5-A43E 
       14.30        13.94         4.21         3.88        34.85        30.25 
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
        8.94         4.70        32.61        21.01         3.32         7.17 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.13         7.43         2.60         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NS TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ 
       16.47        13.41        33.11         7.59         7.04         6.35 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IG-A3I8 TCGA-IG-A3QL 
        7.00        20.02        46.19        18.21        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.78         2.63        20.12         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
        0.79        23.41         9.96        14.50        12.16        68.02 
TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       15.48         7.40        13.55         5.92        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       12.33        13.15        15.35        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.76        12.59        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO 
       12.03        12.85        12.26        20.38         3.42        25.81 
TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       27.09        18.31         8.12        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
       18.05         9.17        15.91        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN 
        2.10         2.66 

$`3P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB 
       16.24        32.45         7.69        14.86       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
       47.38        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OQ 
       18.28        24.00        26.33        19.99        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88Y 
        3.16        58.59         4.90        29.00        22.82         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM 
        3.75         3.02        55.50        13.48        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
       10.36         7.82         7.99         5.06        16.31        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-ZR-A9CJ 
        5.29        16.44         9.27         8.98        22.82        19.73 
TCGA-IC-A6RF TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FA 
       15.68        18.64         9.30        12.82         4.67        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
       47.93        25.12        21.37        10.85        10.45        12.66 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A9 TCGA-Q9-A6FU 
       13.38        12.59        13.25        12.59        11.54         5.16 
TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA7B TCGA-XP-A8T8 
       15.35        12.43         1.55        28.11        11.24        14.37 
TCGA-Z6-A9VB 
        1.32 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.13              0.30 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            68.02            122.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            12.85             13.38 
[1] "0.1 - 68.0 (12.8)"  "0.3 - 122.1 (13.4)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         4        1        3        1        34        15
  3P LOSS WILD-TYPE       4        4        3        0        13        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED          10          9          3          3        3
  3P LOSS WILD-TYPE        15          5          6          4        2
                   vv
clus                STAGE IVA
  3P LOSS MUTATED           1
  3P LOSS WILD-TYPE         3
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  4                 4
  STAGE IA                 1                 4
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               34                13
  STAGE IIB               15                16
  STAGE III               10                15
  STAGE IIIA               9                 5
  STAGE IIIB               3                 6
  STAGE IIIC               3                 4
  STAGE IV                 3                 2
  STAGE IVA                1                 3
[1] 12  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                T0+T1 T2 T3 T4
  3P LOSS MUTATED      14 26 46  3
  3P LOSS WILD-TYPE    18 17 41  2
D46V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              14                18
  T2                 26                17
  T3                 46                41
  T4                  3                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3P LOSS MUTATED   50 30  5  3
  3P LOSS WILD-TYPE 27 38  7  5
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              50                27
  N1              30                38
  N2               5                 7
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   78  4
  3P LOSS WILD-TYPE 57  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     78    4
  3P LOSS WILD-TYPE   57    5
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              78                57
  1               4                 5
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   17 76
  3P LOSS WILD-TYPE 10 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     17   76
  3P LOSS WILD-TYPE   10   81
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              17                10
  MALE                76                81
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   64 22
  3P LOSS WILD-TYPE 60 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     64   22
  3P LOSS WILD-TYPE   60   20
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               64                60
  YES              22                20
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   28 65
  3P LOSS WILD-TYPE 60 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     28   65
  3P LOSS WILD-TYPE   60   31
                                   clus
vv                                  3P LOSS MUTATED 3P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  28                60
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              65                31
[1] 2 2
[1] FALSE
D46V11, continuous
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED   78  2  2  3
  3P LOSS WILD-TYPE 59 10  0  4
D46V12, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              78                59
  R1               2                10
  R2               2                 0
  RX               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED      35                         2    49
  3P LOSS WILD-TYPE    11                         3    65
D46V14, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                  35                11
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  49                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    2 56
  3P LOSS WILD-TYPE  4 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2   56
  3P LOSS WILD-TYPE    4   32
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              56                32
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   20 13
  3Q LOSS WILD-TYPE 87 63
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               33               150 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13                63 
$`3Q LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-JY-A938 TCGA-L5-A43E 
       14.30        13.94         4.21        32.45        34.85        30.25 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A8NH TCGA-R6-A6XQ TCGA-RE-A7BO 
       32.61         3.32         7.43        12.92         6.35         7.00 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IG-A3YA TCGA-IG-A5S3 TCGA-L5-A88Z TCGA-LN-A49K 
       46.19        18.21        20.78        23.41         7.40         5.92 
TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.33        15.35        12.46        12.85         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A9FO TCGA-LN-A9FR TCGA-VR-A8EP TCGA-VR-A8EZ 
       25.25        12.23         0.13        12.26        27.09        18.18 
TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       25.08         3.42         2.10 

$`3Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB 
       16.24         7.69         3.88        14.86       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
       47.38        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
       18.28         8.94        24.00        26.33         4.70        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y 
        4.90        29.00         7.13        22.82         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       27.12        83.24        52.57        46.09        10.36        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         7.99         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       12.69        20.02         5.29        16.44         9.27         8.98 
TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       22.82        19.73        15.68        33.27        35.21         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
        0.79        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NK 
        0.30         4.31        47.93        15.48        25.12        13.55 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       21.37        10.85        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.38        13.15        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        13.22        10.52        12.00        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FU TCGA-S8-A6BW 
       13.38        13.18        12.03        12.85         5.16        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        3.42        15.35        25.81        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        33.70        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
        9.17        15.91        41.23        14.37         1.32         2.66 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.13              0.30 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            46.19            122.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            12.85             13.18 
[1] "0.1 - 46.2 (12.8)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        0        0        1         9        10
  3Q LOSS WILD-TYPE       6        5        6        0        38        21
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           2          2          1          2        2
  3Q LOSS WILD-TYPE        23         12          8          5        3
                   vv
clus                STAGE IVA
  3Q LOSS MUTATED           0
  3Q LOSS WILD-TYPE         4
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 1                 0
  STAGE IIA                9                38
  STAGE IIB               10                21
  STAGE III                2                23
  STAGE IIIA               2                12
  STAGE IIIB               1                 8
  STAGE IIIC               2                 5
  STAGE IV                 2                 3
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  3Q LOSS MUTATED       8  8 15  1
  3Q LOSS WILD-TYPE    24 35 72  4
D47V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1               8                24
  T2                  8                35
  T3                 15                72
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3Q LOSS MUTATED   16 13  1  2
  3Q LOSS WILD-TYPE 61 55 11  6
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              16                61
  N1              13                55
  N2               1                11
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    29   2
  3Q LOSS WILD-TYPE 106   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     29    2
  3Q LOSS WILD-TYPE  106    7
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              29               106
  1               2                 7
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3  30
  3Q LOSS WILD-TYPE  24 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3   30
  3Q LOSS WILD-TYPE   24  127
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                30               127
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   25  6
  3Q LOSS WILD-TYPE 99 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     25    6
  3Q LOSS WILD-TYPE   99   36
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               25                99
  YES               6                36
[1] 2 2
[1] FALSE
D47V9, continuous
D47V10, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   14 19
  3Q LOSS WILD-TYPE 74 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     14   19
  3Q LOSS WILD-TYPE   74   77
                                   clus
vv                                  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  14                74
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              19                77
[1] 2 2
[1] FALSE
D47V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    25   1   1   1
  3Q LOSS WILD-TYPE 112  11   1   6
D47V12, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              25               112
  R1               1                11
  R2               1                 1
  RX               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED      11                         1    17
  3Q LOSS WILD-TYPE    35                         4    97
D47V14, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                  11                35
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  17                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V15, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1 18
  3Q LOSS WILD-TYPE  5 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   18
  3Q LOSS WILD-TYPE    5   70
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              18                70
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   60 44
  4P LOSS WILD-TYPE 47 32
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              104                79 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               44                32 
$`4P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A4QS TCGA-JY-A6FB TCGA-JY-A6FH 
       16.24         4.21        32.45         3.88        60.39        47.38 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       23.18        25.22         3.16         8.94        24.00         4.70 
TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A891 
       21.01         3.16         4.90         7.13         7.43         3.75 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS 
       35.97        12.92        16.47        13.22         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       27.12        46.09        10.36         7.99         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        7.04         6.35         2.89         2.30        12.69         7.00 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-IG-A3I8 
       16.44         9.27         8.98        22.82        46.19        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
       35.21         0.85        20.78        20.12        18.64         0.53 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        12.82         9.96         4.67        12.16        44.75 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        7.40        13.55         5.92        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.38        15.35        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.76        12.85        15.52        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 
       25.25        10.52        12.00        12.23        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC 
       13.18         0.13        12.85        12.26        20.38         3.42 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T8 
       18.18        52.27        18.05        11.24        15.91        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB 
        3.42         1.32 

$`4P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A938 
       31.27         7.63         7.69        14.86       122.10        34.85 
TCGA-JY-A939 TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OF TCGA-L5-A4OH 
       21.70        31.56        30.25        18.28        26.33        32.61 
TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       19.99        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE 
       29.00        22.82         2.60         0.36         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NV 
        2.66        13.48         7.76         5.49        83.24        52.57 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       33.11         7.82        16.31        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF 
       15.78        20.02         5.29        18.21        19.73        15.68 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FD 
        2.63         9.30        17.03        23.41        14.50        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49O 
       47.93        15.48        25.12        21.37        10.85        13.41 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.33        13.15        12.59        12.46        12.59        22.39 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HY TCGA-LN-A9FP TCGA-Q9-A6FU TCGA-V5-AASV 
       11.54         4.47        12.03        12.03         5.16        15.35 
TCGA-VR-A8EO TCGA-VR-A8EY TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE 
       25.81        33.70         9.17        25.08        41.23         2.10 
TCGA-Z6-AAPN 
        2.66 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.30 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            60.39            122.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           12.675            15.480 
[1] "0.1 - 60.4 (12.7)"  "0.3 - 122.1 (15.5)"
[1] "hr=" "1.4"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         4        1        4        1        26        16
  4P LOSS WILD-TYPE       4        4        2        0        21        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED          16          8          7          2        4
  4P LOSS WILD-TYPE         9          6          2          5        1
                   vv
clus                STAGE IVA
  4P LOSS MUTATED           2
  4P LOSS WILD-TYPE         2
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  4                 4
  STAGE IA                 1                 4
  STAGE IB                 4                 2
  STAGE II                 1                 0
  STAGE IIA               26                21
  STAGE IIB               16                15
  STAGE III               16                 9
  STAGE IIIA               8                 6
  STAGE IIIB               7                 2
  STAGE IIIC               2                 5
  STAGE IV                 4                 1
  STAGE IVA                2                 2
[1] 12  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                T0+T1 T2 T3 T4
  4P LOSS MUTATED      14 29 46  4
  4P LOSS WILD-TYPE    18 14 41  1
D48V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              14                18
  T2                 29                14
  T3                 46                41
  T4                  4                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4P LOSS MUTATED   41 40  9  3
  4P LOSS WILD-TYPE 36 28  3  5
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              41                36
  N1              40                28
  N2               9                 3
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   82  6
  4P LOSS WILD-TYPE 53  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     82    6
  4P LOSS WILD-TYPE   53    3
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              82                53
  1               6                 3
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   13 92
  4P LOSS WILD-TYPE 14 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     13   92
  4P LOSS WILD-TYPE   14   65
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              13                14
  MALE                92                65
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   68 26
  4P LOSS WILD-TYPE 56 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     68   26
  4P LOSS WILD-TYPE   56   16
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               68                56
  YES              26                16
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   47 58
  4P LOSS WILD-TYPE 41 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     47   58
  4P LOSS WILD-TYPE   41   38
                                   clus
vv                                  4P LOSS MUTATED 4P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  47                41
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              58                38
[1] 2 2
[1] FALSE
D48V11, continuous
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED   78  9  1  2
  4P LOSS WILD-TYPE 59  3  1  5
D48V12, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              78                59
  R1               9                 3
  R2               1                 1
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED      33                         2    56
  4P LOSS WILD-TYPE    13                         3    58
D48V14, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                  33                13
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  56                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    2 55
  4P LOSS WILD-TYPE  4 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2   55
  4P LOSS WILD-TYPE    4   33
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              55                33
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   45 41
  4Q LOSS WILD-TYPE 62 35
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               86                97 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               41                35 
$`4Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A4QS TCGA-JY-A6FB TCGA-JY-A6FH 
       16.24         4.21        32.45         3.88        60.39        47.38 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       23.18        25.22         3.16         8.94        24.00         4.70 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A8NG 
        3.16         4.90         7.13         7.43         3.75        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       12.92        16.47        13.22         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       83.24        46.09        10.36         7.99         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04        38.40         6.35         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
       12.69         7.00        16.44         9.27         8.98        22.82 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 
       33.27        35.21         0.85         0.53         0.79        12.82 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-L5-A43J TCGA-L5-A88S TCGA-L5-A88Z TCGA-LN-A49K 
        4.67        44.75         4.31        15.48         7.40         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 
       10.45        12.66        13.38        15.35        13.25        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.76        12.85        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FQ TCGA-LN-A9FR 
       10.52        12.00        12.23        13.18        12.85        12.26 
TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 
       20.38        27.09         1.55        28.11        18.18        52.27 
TCGA-VR-AA7B TCGA-VR-AA7I 
       11.24        15.91 

$`4Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A938 
       31.27         7.63         7.69        14.86       122.10        34.85 
TCGA-JY-A939 TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OF TCGA-L5-A4OH 
       21.70        31.56        30.25        18.28        26.33        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 
       58.59        29.00        22.82         2.60         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NV 
       55.50         2.66        13.48         7.76         5.49        52.57 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-S8-A6BV 
       33.11         7.82        16.31        53.95        15.78        20.02 
TCGA-V5-A7RB TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3YA 
        5.29        46.19        18.21        19.73        15.68        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
        2.63        20.12        18.64         9.30        17.03        23.41 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        9.96        14.50        12.16        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A8NK 
       24.03         6.28         0.30        47.93        25.12        13.55 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       21.37        10.85        12.43        13.41        12.33        13.15 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.59        12.62        12.46        12.49        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A8I1 
       15.52        11.54        13.22        12.03        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO 
        0.13        12.03         5.16         3.42        15.35        25.81 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7D 
       12.43        18.31         8.12        33.70        18.05         9.17 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.53              0.13 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            83.24            122.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           12.625            14.370 
[1] "0.5 - 83.2 (12.6)"  "0.1 - 122.1 (14.4)"
[1] "hr=" "1.5"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         3        1        5        1        18        11
  4Q LOSS WILD-TYPE       5        4        1        0        29        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED          15          4          6          2        4
  4Q LOSS WILD-TYPE        10         10          3          5        1
                   vv
clus                STAGE IVA
  4Q LOSS MUTATED           2
  4Q LOSS WILD-TYPE         2
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 1                 4
  STAGE IB                 5                 1
  STAGE II                 1                 0
  STAGE IIA               18                29
  STAGE IIB               11                20
  STAGE III               15                10
  STAGE IIIA               4                10
  STAGE IIIB               6                 3
  STAGE IIIC               2                 5
  STAGE IV                 4                 1
  STAGE IVA                2                 2
[1] 12  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                T0+T1 T2 T3 T4
  4Q LOSS MUTATED      10 20 42  2
  4Q LOSS WILD-TYPE    22 23 45  3
D49V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              10                22
  T2                 20                23
  T3                 42                45
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4Q LOSS MUTATED   32 32  7  3
  4Q LOSS WILD-TYPE 45 36  5  5
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              32                45
  N1              32                36
  N2               7                 5
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   61  6
  4Q LOSS WILD-TYPE 74  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     61    6
  4Q LOSS WILD-TYPE   74    3
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              61                74
  1               6                 3
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9 78
  4Q LOSS WILD-TYPE 18 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9   78
  4Q LOSS WILD-TYPE   18   79
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               9                18
  MALE                78                79
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   59 16
  4Q LOSS WILD-TYPE 65 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     59   16
  4Q LOSS WILD-TYPE   65   26
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               59                65
  YES              16                26
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   48 39
  4Q LOSS WILD-TYPE 40 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     48   39
  4Q LOSS WILD-TYPE   40   57
                                   clus
vv                                  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  48                40
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              39                57
[1] 2 2
[1] FALSE
D49V11, continuous
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   60  7  2  3
  4Q LOSS WILD-TYPE 77  5  0  4
D49V12, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              60                77
  R1               7                 5
  R2               2                 0
  RX               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED      25                         0    49
  4Q LOSS WILD-TYPE    21                         5    65
D49V14, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                  25                21
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  49                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    2 41
  4Q LOSS WILD-TYPE  4 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   41
  4Q LOSS WILD-TYPE    4   47
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              41                47
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED   27 19
  5P LOSS WILD-TYPE 80 57
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               46               137 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               19                57 
$`5P LOSS MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A4QS 
       58.55         7.63        13.94         8.94         4.21         3.88 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
      122.10        60.39        30.25        24.00        26.33         4.70 
TCGA-L5-A4OJ TCGA-L5-A4OS TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       21.01        58.59         2.60         3.75         3.02         2.66 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.49         8.71        27.12        33.11        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-AASW 
        9.30         2.89         2.30        12.69        20.02         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IG-A3QL TCGA-IG-A50L 
        8.98        22.82        46.19        18.21        35.21         0.53 
TCGA-IG-A51D TCGA-IG-A8O2 TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A4A8 
       17.03         4.67         5.92        10.45        12.59        15.52 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-VR-A8ER 
       10.52        12.03        13.38        12.43 

$`5P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        31.27        14.30         5.92        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        7.69        14.86        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OH 
       31.56        25.22         3.16        18.28         8.94        32.61 
TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       19.99        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Y 
        4.90        29.00         7.13         7.43        22.82         0.36 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        7.76        13.41        83.24        52.57        46.09        10.36 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         7.99         7.59         5.06        16.31         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-ZR-A9CJ 
       53.95        15.78         7.00         5.29        16.44        19.73 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       15.68        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
       18.64         9.30         0.79        23.41        12.82         9.96 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S 
       24.03         6.28         0.30         4.31        47.93        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49M 
       25.12         7.40        13.55        21.37        10.85        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        25.25        12.00        12.23        13.18 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU 
       13.18         0.13        12.03        12.85        12.26         5.16 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET 
       20.38         3.42        15.35        25.81        27.09         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       14.37         3.42         2.10         1.32         2.66 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.53              0.13 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           122.10             83.24 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            12.23             13.22 
[1] "0.5 - 122.1 (12.2)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         7        0        0        0         8         6
  5P LOSS WILD-TYPE       1        5        6        1        39        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           9          2          3          0        0
  5P LOSS WILD-TYPE        16         12          6          7        5
                   vv
clus                STAGE IVA
  5P LOSS MUTATED           1
  5P LOSS WILD-TYPE         3
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  7                 1
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                8                39
  STAGE IIB                6                25
  STAGE III                9                16
  STAGE IIIA               2                12
  STAGE IIIB               3                 6
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                1                 3
[1] 12  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                T0+T1 T2 T3 T4
  5P LOSS MUTATED      13  6 18  1
  5P LOSS WILD-TYPE    19 37 69  4
D50V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              13                19
  T2                  6                37
  T3                 18                69
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5P LOSS MUTATED   17 18  3  0
  5P LOSS WILD-TYPE 60 50  9  8
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              17                60
  N1              18                50
  N2               3                 9
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    32   1
  5P LOSS WILD-TYPE 103   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     32    1
  5P LOSS WILD-TYPE  103    8
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              32               103
  1               1                 8
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5  41
  5P LOSS WILD-TYPE  22 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5   41
  5P LOSS WILD-TYPE   22  116
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                22
  MALE                41               116
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                 0  1
  5P LOSS MUTATED   33  8
  5P LOSS WILD-TYPE 91 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     33    8
  5P LOSS WILD-TYPE   91   34
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               33                91
  YES               8                34
[1] 2 2
[1] FALSE
D50V9, continuous
D50V10, binary
                   cls
clus                 0  1
  5P LOSS MUTATED   34 12
  5P LOSS WILD-TYPE 54 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     34   12
  5P LOSS WILD-TYPE   54   84
                                   clus
vv                                  5P LOSS MUTATED 5P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  34                54
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              12                84
[1] 2 2
[1] FALSE
D50V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    31   2   0   2
  5P LOSS WILD-TYPE 106  10   2   5
D50V12, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              31               106
  R1               2                10
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       9                         0    29
  5P LOSS WILD-TYPE    37                         5    85
D50V14, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   9                37
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  29                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V15, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2 20
  5P LOSS WILD-TYPE  4 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   20
  5P LOSS WILD-TYPE    4   68
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              20                68
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   51 35
  5Q LOSS WILD-TYPE 56 41
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               86                97 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               35                41 
$`5Q LOSS MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93D 
       32.45         3.88       122.10        60.39        47.38        31.56 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OP 
       30.25        24.00        26.33         4.70        21.01         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y 
        3.16        58.59         4.90         7.13         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.75         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-M9-A5M8 
        5.49         8.71        13.41        27.12        52.57        33.11 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       38.40         6.35         9.30         2.89         2.30        12.69 
TCGA-S8-A6BV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR 
       20.02         9.27         8.98        22.82        46.19        18.21 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A8O2 
       35.21         2.63        20.12        18.64         0.53         4.67 
TCGA-IG-A97H TCGA-L5-A4OM TCGA-L5-A8NK TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       14.50        47.93        13.55        10.85         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49U TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.43        15.35        12.49        22.39        15.52        12.33 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.33        10.52        12.03        13.18        13.38        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-VR-A8EO TCGA-VR-A8EP 
       12.85        12.26         5.16        20.38        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-XP-A8T6 TCGA-Z6-A8JE 
       12.43         8.12        28.11        52.27        25.08         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

$`5Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IC-A6RE TCGA-IG-A7DP 
       25.78        31.27        14.30         5.92         7.69        14.86 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I 
       34.85        21.70        23.18        25.22         3.16        18.28 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        8.94        32.61        19.99        18.35         3.32         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       29.00         7.43        22.82        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-Q9-A6FW TCGA-R6-A6DN 
        7.76        83.24        46.09        10.36         7.82         7.99 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 
        7.59         5.06        16.31         7.04        53.95        15.78 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 
        7.00         5.29        16.44        19.73        15.68        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.85        20.78         9.30        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       12.82         9.96        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88S 
       41.52        24.03         6.28         0.30         4.31        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P 
       25.12         7.40        21.37        12.66        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.59        12.76        12.59        12.85        11.54        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-LN-A9FP 
        4.47        25.25        12.00        12.23         0.13        12.03 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ 
        3.42        15.35         1.55        18.31        33.70        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 
       18.05        11.24         9.17        15.91        41.23        14.37 
TCGA-Z6-A8JD 
        3.42 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.36              0.13 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           122.10             83.24 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           12.885            13.220 
[1] "0.4 - 122.1 (12.9)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         7        3        1        0        19        14
  5Q LOSS WILD-TYPE       1        2        5        1        28        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED          11          7          6          1        2
  5Q LOSS WILD-TYPE        14          7          3          6        3
                   vv
clus                STAGE IVA
  5Q LOSS MUTATED           3
  5Q LOSS WILD-TYPE         1
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  7                 1
  STAGE IA                 3                 2
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA               19                28
  STAGE IIB               14                17
  STAGE III               11                14
  STAGE IIIA               7                 7
  STAGE IIIB               6                 3
  STAGE IIIC               1                 6
  STAGE IV                 2                 3
  STAGE IVA                3                 1
[1] 12  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                T0+T1 T2 T3 T4
  5Q LOSS MUTATED      18 19 39  1
  5Q LOSS WILD-TYPE    14 24 48  4
D51V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              18                14
  T2                 19                24
  T3                 39                48
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5Q LOSS MUTATED   34 35  6  1
  5Q LOSS WILD-TYPE 43 33  6  7
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              34                43
  N1              35                33
  N2               6                 6
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   62  5
  5Q LOSS WILD-TYPE 73  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     62    5
  5Q LOSS WILD-TYPE   73    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              62                73
  1               5                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   11 75
  5Q LOSS WILD-TYPE 16 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11   75
  5Q LOSS WILD-TYPE   16   82
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              11                16
  MALE                75                82
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   58 18
  5Q LOSS WILD-TYPE 66 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     58   18
  5Q LOSS WILD-TYPE   66   24
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               58                66
  YES              18                24
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   48 38
  5Q LOSS WILD-TYPE 40 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     48   38
  5Q LOSS WILD-TYPE   40   58
                                   clus
vv                                  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  48                40
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              38                58
[1] 2 2
[1] FALSE
D51V11, continuous
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED   65  6  0  3
  5Q LOSS WILD-TYPE 72  6  2  4
D51V12, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              65                72
  R1               6                 6
  R2               0                 2
  RX               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED      20                         2    52
  5Q LOSS WILD-TYPE    26                         3    62
D51V14, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                  20                26
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  52                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    3 38
  5Q LOSS WILD-TYPE  3 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   38
  5Q LOSS WILD-TYPE    3   50
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              38                50
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   25 13
  6P LOSS WILD-TYPE 82 63
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               145 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               13                63 
$`6P LOSS MUTATED`
TCGA-JY-A6FB TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OR 
       60.39        23.18         3.16         8.94         4.70         3.16 
TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-R6-A8WC TCGA-R6-A8WG 
        0.36        16.47        83.24        52.57         2.30        12.69 
TCGA-S8-A6BV TCGA-V5-AASW TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3QL 
       20.02         9.27        22.82        19.73        33.27        35.21 
TCGA-IG-A50L TCGA-IG-A5S3 TCGA-L5-A43J TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49N 
        0.53        23.41         4.31        13.55         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A5U7 TCGA-LN-A7HZ 
       13.41        13.25        12.59        12.49        25.25        13.18 
TCGA-LN-A8I0 TCGA-V5-A7RC TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-XP-A8T6 
       13.38         3.42        12.43         8.12        18.18        25.08 
TCGA-Z6-A8JD TCGA-Z6-AAPN 
        3.42         2.66 

$`6P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
        3.88        14.86       122.10        47.38        34.85        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OF 
       31.56        25.22        30.25        18.28        24.00        26.33 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       22.82         2.60         3.75         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        12.92        13.48        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
        8.71        13.41        27.12        46.09        10.36        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         7.99         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR 
        7.00         5.29        16.44         8.98        46.19        18.21 
TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       15.68         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        9.30        17.03         0.79        12.82         9.96         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
       24.03         6.28         0.30        47.93        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P 
        7.40        21.37        10.85        10.45        12.66        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        15.35        12.59        12.62        12.46 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.23        12.03        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
       12.26         5.16        20.38        15.35        25.81        27.09 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G 
        1.55        18.31        28.11        33.70        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       11.24         9.17        15.91        41.23        14.37         2.10 
TCGA-Z6-A9VB 
        1.32 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.36              0.13 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            83.24            122.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           12.935            13.150 
[1] "0.4 - 83.2 (12.9)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.2"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         2        1        0        0        14         5
  6P LOSS WILD-TYPE       6        4        6        1        33        26
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           4          2          2          2        0
  6P LOSS WILD-TYPE        21         12          7          5        5
                   vv
clus                STAGE IVA
  6P LOSS MUTATED           0
  6P LOSS WILD-TYPE         4
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 1                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA               14                33
  STAGE IIB                5                26
  STAGE III                4                21
  STAGE IIIA               2                12
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  6P LOSS MUTATED       4  8 21  1
  6P LOSS WILD-TYPE    28 35 66  4
D52V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               4                28
  T2                  8                35
  T3                 21                66
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6P LOSS MUTATED   21  8  3  2
  6P LOSS WILD-TYPE 56 60  9  6
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              21                56
  N1               8                60
  N2               3                 9
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    28   0
  6P LOSS WILD-TYPE 107   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     28    0
  6P LOSS WILD-TYPE  107    9
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              28               107
  1               0                 9
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  34
  6P LOSS WILD-TYPE  22 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   34
  6P LOSS WILD-TYPE   22  123
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               5                22
  MALE                34               123
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   26  7
  6P LOSS WILD-TYPE 98 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     26    7
  6P LOSS WILD-TYPE   98   35
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               26                98
  YES               7                35
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   16 23
  6P LOSS WILD-TYPE 72 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     16   23
  6P LOSS WILD-TYPE   72   73
                                   clus
vv                                  6P LOSS MUTATED 6P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  16                72
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              23                73
[1] 2 2
[1] FALSE
D52V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    26   3   0   2
  6P LOSS WILD-TYPE 111   9   2   5
D52V12, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              26               111
  R1               3                 9
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED      13                         2    22
  6P LOSS WILD-TYPE    33                         3    92
D52V14, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                  13                33
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  22                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    2 20
  6P LOSS WILD-TYPE  4 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   20
  6P LOSS WILD-TYPE    4   68
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              20                68
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   22 16
  6Q LOSS WILD-TYPE 85 60
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               38               145 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16                60 
$`6Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OR 
       25.78        47.38        25.22         3.16         8.94         3.16 
TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-R6-A6XG 
        0.36        16.47        13.41        83.24        52.57        38.40 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-AASW TCGA-VR-A8EQ TCGA-ZR-A9CJ 
        2.30        12.69        20.02         9.27        22.82        19.73 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49O 
       33.27        35.21         4.67        13.55         5.92        13.41 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 
       13.25        12.59        12.49        22.39        13.22        25.25 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       20.38         3.42        12.43         8.12        28.11        18.18 
TCGA-XP-A8T6 TCGA-Z6-A8JD 
       25.08         3.42 

$`6Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        8.94        16.24         4.21        32.45         7.69         3.88 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       14.86       122.10        60.39        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       31.56        30.25        18.28        24.00        26.33         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       22.82         2.60         3.75         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        12.92        13.48        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
        8.71        27.12        46.09        10.36        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.99         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB 
       53.95         9.30        15.78         2.89         7.00         5.29 
TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3Y9 
       16.44         8.98        46.19        18.21        15.68         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97H 
       17.03         0.79        23.41        12.82         9.96        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
        6.28         0.30         4.31        47.93        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        7.40        21.37        10.85        10.45        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33         4.47        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
       12.85        12.26         5.16        15.35        25.81        27.09 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
        1.55        18.31        33.70        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
        9.17        15.91        41.23        14.37         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.36              0.13 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            83.24            122.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            13.48             12.82 
[1] "0.4 - 83.2 (13.5)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0        1        1        0        13         4
  6Q LOSS WILD-TYPE       8        4        5        1        34        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           5          2          2          2        0
  6Q LOSS WILD-TYPE        20         12          7          5        5
                   vv
clus                STAGE IVA
  6Q LOSS MUTATED           1
  6Q LOSS WILD-TYPE         3
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 1                 4
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA               13                34
  STAGE IIB                4                27
  STAGE III                5                20
  STAGE IIIA               2                12
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 0                 5
  STAGE IVA                1                 3
[1] 12  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                T0+T1 T2 T3 T4
  6Q LOSS MUTATED       3  9 20  1
  6Q LOSS WILD-TYPE    29 34 67  4
D53V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               3                29
  T2                  9                34
  T3                 20                67
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6Q LOSS MUTATED   18 10  3  2
  6Q LOSS WILD-TYPE 59 58  9  6
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              18                59
  N1              10                58
  N2               3                 9
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    26   1
  6Q LOSS WILD-TYPE 109   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     26    1
  6Q LOSS WILD-TYPE  109    8
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              26               109
  1               1                 8
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3  36
  6Q LOSS WILD-TYPE  24 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   36
  6Q LOSS WILD-TYPE   24  121
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                36               121
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   26  8
  6Q LOSS WILD-TYPE 98 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     26    8
  6Q LOSS WILD-TYPE   98   34
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               26                98
  YES               8                34
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   18 21
  6Q LOSS WILD-TYPE 70 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18   21
  6Q LOSS WILD-TYPE   70   75
                                   clus
vv                                  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  18                70
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              21                75
[1] 2 2
[1] FALSE
D53V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    26   4   0   1
  6Q LOSS WILD-TYPE 111   8   2   6
D53V12, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              26               111
  R1               4                 8
  R2               0                 2
  RX               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED      11                         2    22
  6Q LOSS WILD-TYPE    35                         3    92
D53V14, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                  11                35
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  22                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    2 19
  6Q LOSS WILD-TYPE  4 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   19
  6Q LOSS WILD-TYPE    4   69
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              19                69
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     7   6
  7P LOSS WILD-TYPE 100  70
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               170 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6                70 
$`7P LOSS MUTATED`
TCGA-2H-A9GI TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NS TCGA-IG-A3Y9 
       14.30        29.00        55.50        13.48        13.41         0.85 
TCGA-JY-A6FD TCGA-L5-A4OM TCGA-LN-A49L TCGA-LN-A4A8 TCGA-LN-A7HY TCGA-Q9-A6FU 
       68.02        47.93        10.45        15.52        12.03         5.16 
TCGA-VR-A8EO 
       25.81 

$`7P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        8.94        16.24         4.21        32.45         7.69         3.88 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       14.86       122.10        60.39        47.38        34.85        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I 
       23.18        31.56        25.22         3.16        30.25        18.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00        26.33         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
       58.59         4.90         7.13         7.43        22.82         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         3.75         3.02         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT 
       16.47        13.22         7.76         5.49         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       83.24        52.57        46.09        10.36        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.99         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.02         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF 
        8.98        22.82        46.19        18.21        19.73        15.68 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE 
        9.96         4.67        14.50        12.16        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88S 
       41.52        24.03         6.28         0.30         4.31        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K 
       25.12         7.40        13.55        21.37        10.85         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        12.85        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.00        12.23        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       12.03        12.85        12.26        20.38         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.85              0.13 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            68.02            122.10 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            14.30             12.85 
[1] "0.8 - 68.0 (14.3)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.3"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        1        0        0         5         2
  7P LOSS WILD-TYPE       8        4        6        1        42        29
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           3          1          1          0        0
  7P LOSS WILD-TYPE        22         13          8          7        5
                   vv
clus                STAGE IVA
  7P LOSS MUTATED           0
  7P LOSS WILD-TYPE         4
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 1                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                5                42
  STAGE IIB                2                29
  STAGE III                3                22
  STAGE IIIA               1                13
  STAGE IIIB               1                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  7P LOSS MUTATED       1  3  8  1
  7P LOSS WILD-TYPE    31 40 79  4
D54V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               1                31
  T2                  3                40
  T3                  8                79
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7P LOSS MUTATED    8  4  1  0
  7P LOSS WILD-TYPE 69 64 11  8
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               8                69
  N1               4                64
  N2               1                11
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    12   0
  7P LOSS WILD-TYPE 123   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     12    0
  7P LOSS WILD-TYPE  123    9
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              12               123
  1               0                 9
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3  10
  7P LOSS WILD-TYPE  24 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3   10
  7P LOSS WILD-TYPE   24  147
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3                24
  MALE                10               147
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    10   3
  7P LOSS WILD-TYPE 114  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10    3
  7P LOSS WILD-TYPE  114   39
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               10               114
  YES               3                39
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    5  8
  7P LOSS WILD-TYPE 83 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5    8
  7P LOSS WILD-TYPE   83   88
                                   clus
vv                                  7P LOSS MUTATED 7P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   5                83
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               8                88
[1] 2 2
[1] FALSE
D54V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    12   0   0   1
  7P LOSS WILD-TYPE 125  12   2   6
D54V12, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              12               125
  R1               0                12
  R2               0                 2
  RX               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       4                         0     8
  7P LOSS WILD-TYPE    42                         5   106
D54V14, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   4                42
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   8               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    0  5
  7P LOSS WILD-TYPE  6 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    5
  7P LOSS WILD-TYPE    6   83
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5                83
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED   12 10
  7Q LOSS WILD-TYPE 95 66
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               22               161 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10                66 
$`7Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NI 
       25.78        14.30         5.92        29.00        55.50        13.48 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-V5-AASX TCGA-IG-A3Y9 
        8.71        13.41        33.11         5.06         8.98         0.85 
TCGA-IG-A5B8 TCGA-JY-A6FD TCGA-L5-A8NK TCGA-LN-A49L TCGA-LN-A49X TCGA-LN-A7HY 
        0.79        68.02        13.55        10.45        12.62        12.03 
TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-AA7I TCGA-Z6-AAPN 
       25.81         1.55        15.91         2.66 

$`7Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 
        4.21        32.45         7.69         3.88        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       60.39        47.38        34.85        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       25.22         3.16        30.25        18.28         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       26.33         4.70        32.61        19.99        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
        7.13         7.43        22.82         2.60         0.36         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL 
        3.02         2.66        35.97        12.92        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         5.49        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       10.36         7.82         7.99         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.02         5.29        16.44 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF 
        9.27        22.82        46.19        18.21        19.73        15.68 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        12.16        44.75         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S 
       24.03         6.28         0.30         4.31        47.93        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M 
       25.12         7.40        21.37        10.85         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       12.85        12.26         5.16        20.38         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       27.09        12.43        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 
       18.18        52.27        18.05        11.24         9.17        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       41.23        14.37         3.42         2.10         1.32 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.79              0.13 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            68.02            122.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           13.015            13.150 
[1] "0.8 - 68.0 (13.0)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         0        0        1        0         9         2
  7Q LOSS WILD-TYPE       8        5        5        1        38        29
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           7          1          0          0        0
  7Q LOSS WILD-TYPE        18         13          9          7        5
                   vv
clus                STAGE IVA
  7Q LOSS MUTATED           0
  7Q LOSS WILD-TYPE         4
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 5
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                9                38
  STAGE IIB                2                29
  STAGE III                7                18
  STAGE IIIA               1                13
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  7Q LOSS MUTATED       0  3 15  2
  7Q LOSS WILD-TYPE    32 40 72  3
D55V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               0                32
  T2                  3                40
  T3                 15                72
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7Q LOSS MUTATED   13  7  0  0
  7Q LOSS WILD-TYPE 64 61 12  8
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              13                64
  N1               7                61
  N2               0                12
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    20   0
  7Q LOSS WILD-TYPE 115   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     20    0
  7Q LOSS WILD-TYPE  115    9
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              20               115
  1               0                 9
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3  19
  7Q LOSS WILD-TYPE  24 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3   19
  7Q LOSS WILD-TYPE   24  138
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                19               138
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    16   4
  7Q LOSS WILD-TYPE 108  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     16    4
  7Q LOSS WILD-TYPE  108   38
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               16               108
  YES               4                38
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED   11 11
  7Q LOSS WILD-TYPE 77 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11   11
  7Q LOSS WILD-TYPE   77   85
                                   clus
vv                                  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  11                77
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              11                85
[1] 2 2
[1] FALSE
D55V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    16   3   1   0
  7Q LOSS WILD-TYPE 121   9   1   7
D55V12, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              16               121
  R1               3                 9
  R2               1                 1
  RX               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       4                         0    13
  7Q LOSS WILD-TYPE    42                         5   101
D55V14, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   4                42
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  13               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V15, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    0  8
  7Q LOSS WILD-TYPE  6 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    8
  7Q LOSS WILD-TYPE    6   80
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               8                80
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   40 23
  8P LOSS WILD-TYPE 67 53
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               63               120 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               23                53 
$`8P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A6FB 
       25.78         5.92        13.94         7.69         3.88        60.39 
TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       34.85        23.18        25.22         8.94        24.00        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A8NE 
       32.61        21.01         3.32         7.43         3.75        55.50 
TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT TCGA-Q9-A6FW TCGA-R6-A6DN 
        2.66         5.49         8.71        27.12         7.82         7.99 
TCGA-R6-A8WC TCGA-V5-A7RB TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A50L 
        2.30         5.29         0.85         2.63        20.12         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-L5-A88Z 
        0.79        23.41         9.96        14.50        44.75         7.40 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 
       12.66        12.43        12.46        12.59        12.49        22.39 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FQ 
       12.33        13.22        12.33        12.00        13.18        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8ER TCGA-VR-A8EU 
       12.26         5.16        20.38         3.42        12.43        18.31 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       28.11        52.27        18.05         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23         1.32         2.66 

$`8P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        14.30        58.55         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A939 
        4.21        32.45        14.86       122.10        47.38        21.70 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OG TCGA-L5-A4OI 
       31.56         3.16        30.25        18.28         4.70        19.99 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 
       29.00         7.13        22.82         2.60         0.36         3.02 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       13.41        83.24        52.57        46.09        10.36        33.11 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
       20.02        16.44         9.27         8.98        22.82        46.19 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
       18.21        19.73        15.68        33.27        35.21        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97I 
       18.64         9.30        17.03        12.82         4.67        12.16 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H 
       68.02         3.68        41.52        24.03         6.28         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NK TCGA-L5-A8NQ 
        4.31        47.93        15.48        25.12        13.55        21.37 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.85         5.92        10.45        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 
       13.15        15.35        12.59        13.25        12.62        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59        12.85        15.52        11.54         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       10.52        12.23        12.03        13.18        13.38         0.13 
TCGA-LN-A9FP TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW 
       12.03        15.35        25.81        27.09         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       33.70        18.18        11.24        14.37         3.42         2.10 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.53              0.13 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            60.39            122.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            12.46             13.38 
[1] "0.5 - 60.4 (12.5)"  "0.1 - 122.1 (13.4)"
[1] "hr=" "1"  
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         3        0        2        0        13        14
  8P LOSS WILD-TYPE       5        5        4        1        34        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           7          8          5          2        1
  8P LOSS WILD-TYPE        18          6          4          5        4
                   vv
clus                STAGE IVA
  8P LOSS MUTATED           2
  8P LOSS WILD-TYPE         2
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 0                 5
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA               13                34
  STAGE IIB               14                17
  STAGE III                7                18
  STAGE IIIA               8                 6
  STAGE IIIB               5                 4
  STAGE IIIC               2                 5
  STAGE IV                 1                 4
  STAGE IVA                2                 2
[1] 12  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                T0+T1 T2 T3 T4
  8P LOSS MUTATED      11 16 30  3
  8P LOSS WILD-TYPE    21 27 57  2
D56V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              11                21
  T2                 16                27
  T3                 30                57
  T4                  3                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8P LOSS MUTATED   22 28  7  2
  8P LOSS WILD-TYPE 55 40  5  6
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              22                55
  N1              28                40
  N2               7                 5
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   52  3
  8P LOSS WILD-TYPE 83  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     52    3
  8P LOSS WILD-TYPE   83    6
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              52                83
  1               3                 6
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     9  54
  8P LOSS WILD-TYPE  18 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      9   54
  8P LOSS WILD-TYPE   18  103
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               9                18
  MALE                54               103
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   46 11
  8P LOSS WILD-TYPE 78 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     46   11
  8P LOSS WILD-TYPE   78   31
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               46                78
  YES              11                31
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   26 37
  8P LOSS WILD-TYPE 62 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     26   37
  8P LOSS WILD-TYPE   62   59
                                   clus
vv                                  8P LOSS MUTATED 8P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  26                62
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              37                59
[1] 2 2
[1] FALSE
D56V11, continuous
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   48  4  1  4
  8P LOSS WILD-TYPE 89  8  1  3
D56V12, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              48                89
  R1               4                 8
  R2               1                 1
  RX               4                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED      17                         2    35
  8P LOSS WILD-TYPE    29                         3    79
D56V14, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                  17                29
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  35                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    3 31
  8P LOSS WILD-TYPE  3 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3   31
  8P LOSS WILD-TYPE    3   57
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              31                57
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED   15  8
  8Q LOSS WILD-TYPE 92 68
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               23               160 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                68 
$`8Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-JY-A6FB TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OF 
       25.78         5.92        60.39        25.22         8.94        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-IG-A5S3 
       32.61        21.01         3.75        55.50         2.66        23.41 
TCGA-JY-A6FA TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW 
       44.75        12.43        12.46        13.22        12.33        12.00 
TCGA-V5-A7RC TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-XP-A8T6 TCGA-Z6-AAPN 
        3.42        28.11        52.27        25.08         2.66 

$`8Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
       16.24         4.21        32.45         7.69         3.88        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
      122.10        47.38        34.85        21.70        23.18        31.56 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
        3.16        30.25        18.28        24.00         4.70        19.99 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        22.82         2.60 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        0.36         3.02        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76         5.49         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       83.24        52.57        46.09        10.36        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.99         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.02         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF 
        8.98        22.82        46.19        18.21        19.73        15.68 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
       18.64         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE 
        9.96         4.67        14.50        12.16        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM 
       41.52        24.03         6.28         0.30         4.31        47.93 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G 
       15.48        25.12         7.40        13.55        21.37        10.85 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
        5.92        10.45        12.66        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       11.54        12.33         4.47        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO 
       12.85        12.26         5.16        20.38        15.35        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       27.09        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       18.18        18.05        11.24         9.17        15.91        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       14.37         3.42         2.10         1.32 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             2.66              0.13 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            60.39            122.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           21.010            12.885 
[1] "2.7 - 60.4 (21.0)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "1.6"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         3        0        0        0         4         7
  8Q LOSS WILD-TYPE       5        5        6        1        43        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           2          2          0          0        0
  8Q LOSS WILD-TYPE        23         12          9          7        5
                   vv
clus                STAGE IVA
  8Q LOSS MUTATED           2
  8Q LOSS WILD-TYPE         2
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                4                43
  STAGE IIB                7                24
  STAGE III                2                23
  STAGE IIIA               2                12
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                2                 2
[1] 12  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                T0+T1 T2 T3 T4
  8Q LOSS MUTATED       6  7  9  0
  8Q LOSS WILD-TYPE    26 36 78  5
D57V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               6                26
  T2                  7                36
  T3                  9                78
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q LOSS MUTATED    9 12  1  0
  8Q LOSS WILD-TYPE 68 56 11  8
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               9                68
  N1              12                56
  N2               1                11
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    18   2
  8Q LOSS WILD-TYPE 117   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     18    2
  8Q LOSS WILD-TYPE  117    7
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              18               117
  1               2                 7
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     3  20
  8Q LOSS WILD-TYPE  24 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3   20
  8Q LOSS WILD-TYPE   24  137
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                20               137
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    20   2
  8Q LOSS WILD-TYPE 104  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     20    2
  8Q LOSS WILD-TYPE  104   40
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               20               104
  YES               2                40
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED   11 12
  8Q LOSS WILD-TYPE 77 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11   12
  8Q LOSS WILD-TYPE   77   84
                                   clus
vv                                  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  11                77
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              12                84
[1] 2 2
[1] FALSE
D57V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    17   2   0   1
  8Q LOSS WILD-TYPE 120  10   2   6
D57V12, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              17               120
  R1               2                10
  R2               0                 2
  RX               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       6                         2    11
  8Q LOSS WILD-TYPE    40                         3   103
D57V14, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   6                40
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  11               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  8
  8Q LOSS WILD-TYPE  5 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    8
  8Q LOSS WILD-TYPE    5   80
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO               8                80
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   62 38
  9P LOSS WILD-TYPE 45 38
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              100                83 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38                38 
$`9P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43C 
        7.69         3.88        60.39        34.85        25.22         3.16 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO 
       18.28         8.94        26.33        32.61        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A891 
        7.17        58.59         7.13         7.43         2.60         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR 
       55.50         2.66        35.97        16.47        13.22         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6L4 
       13.41        83.24        10.36        33.11         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
       38.40         6.35         9.30        15.78         2.30        12.69 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
       20.02         5.29        16.44         9.27         8.98        22.82 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       46.19        18.21        19.73        20.78        20.12        18.64 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.53         0.79        23.41         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-L5-A4OM TCGA-L5-A88S TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       12.16        47.93        15.48        10.45        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.49        12.76        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-V5-A7RC 
       12.03         0.13        12.03        12.26         5.16         3.42 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       25.81        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8Q7 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       52.27        41.23        14.37         3.42 

$`9P LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A7DP 
       58.55         7.63         5.92        13.94        32.45        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43E 
      122.10        47.38        21.70        23.18        31.56        30.25 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR 
       24.00         4.70        19.99        21.01         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NH 
        4.90        29.00        22.82         0.36         3.02        12.92 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
       13.48         7.76         5.49        27.12        52.57        46.09 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 
        7.82         7.99         7.59         7.04        53.95         2.89 
TCGA-RE-A7BO TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
        7.00        15.68        33.27        35.21         0.85         2.63 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        9.30        17.03        12.82        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88W 
       41.52        24.03         6.28         0.30         4.31        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49O 
        7.40        13.55        21.37        10.85         5.92        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U5 
       12.33        13.38        12.59        12.59        11.54         4.47 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-S8-A6BW TCGA-V5-AASV 
       13.18        13.38        13.18        12.85        20.38        15.35 
TCGA-VR-A8EP TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       27.09        33.70        18.18        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       15.91        25.08         2.10         1.32         2.66 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.24            122.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           12.725            13.380 
[1] "0.1 - 83.2 (12.7)"  "0.3 - 122.1 (13.4)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         2        2        3        1        25        19
  9P LOSS WILD-TYPE       6        3        3        0        22        12
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED          15          7          4          3        1
  9P LOSS WILD-TYPE        10          7          5          4        4
                   vv
clus                STAGE IVA
  9P LOSS MUTATED           4
  9P LOSS WILD-TYPE         0
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               25                22
  STAGE IIB               19                12
  STAGE III               15                10
  STAGE IIIA               7                 7
  STAGE IIIB               4                 5
  STAGE IIIC               3                 4
  STAGE IV                 1                 4
  STAGE IVA                4                 0
[1] 12  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                T0+T1 T2 T3 T4
  9P LOSS MUTATED      16 26 46  2
  9P LOSS WILD-TYPE    16 17 41  3
D58V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              16                16
  T2                 26                17
  T3                 46                41
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9P LOSS MUTATED   38 43  5  3
  9P LOSS WILD-TYPE 39 25  7  5
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              38                39
  N1              43                25
  N2               5                 7
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   72  5
  9P LOSS WILD-TYPE 63  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     72    5
  9P LOSS WILD-TYPE   63    4
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              72                63
  1               5                 4
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   10 91
  9P LOSS WILD-TYPE 17 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10   91
  9P LOSS WILD-TYPE   17   66
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              10                17
  MALE                91                66
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   63 27
  9P LOSS WILD-TYPE 61 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     63   27
  9P LOSS WILD-TYPE   61   15
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               63                61
  YES              27                15
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   51 50
  9P LOSS WILD-TYPE 37 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     51   50
  9P LOSS WILD-TYPE   37   46
                                   clus
vv                                  9P LOSS MUTATED 9P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  51                37
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              50                46
[1] 2 2
[1] FALSE
D58V11, continuous
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED   78  4  0  2
  9P LOSS WILD-TYPE 59  8  2  5
D58V12, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              78                59
  R1               4                 8
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED      30                         2    56
  9P LOSS WILD-TYPE    16                         3    58
D58V14, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                  30                16
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  56                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    5 53
  9P LOSS WILD-TYPE  1 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      5   53
  9P LOSS WILD-TYPE    1   35
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 1
  NOT HISPANIC OR LATINO              53                35
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   37 27
  9Q LOSS WILD-TYPE 70 49
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               64               119 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               27                49 
$`9Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IG-A4QS TCGA-JY-A93E TCGA-L5-A43I 
       25.78        31.27        16.24         3.88        25.22        18.28 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A8NE 
        8.94        26.33        58.59         7.13         2.60        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
        2.66        35.97        13.22        13.41        83.24        10.36 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
        5.06        38.40         6.35         9.30        15.78        12.69 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IG-A3Y9 TCGA-IG-A3YA 
        5.29        16.44        18.21        19.73         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
       20.12        18.64         0.79        23.41         9.96         4.67 
TCGA-IG-A97H TCGA-L5-A4OM TCGA-L5-A88S TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       14.50        47.93        15.48        10.45        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 
       13.15        12.46        12.59        12.76        12.85        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.18         0.13 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 
        3.42        25.81         1.55         8.12        28.11        52.27 
TCGA-VR-AA7B TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24        14.37         3.42         2.10 

$`9Q LOSS WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB 
        4.21        32.45         7.69        14.86       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C 
       47.38        34.85        21.70        23.18        31.56         3.16 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       30.25        24.00         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
       29.00         7.43        22.82         0.36         3.75         3.02 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       12.92        13.48        16.47         7.76         5.49         8.71 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       27.12        52.57        46.09        33.11         7.82         7.99 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.59        16.31         7.04        53.95         2.89         2.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
        7.00        20.02         9.27         8.98        22.82        46.19 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L 
       15.68        33.27        35.21         2.63         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       17.03        12.82        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88W 
       41.52        24.03         6.28         0.30         4.31        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49O 
        7.40        13.55        21.37        10.85         5.92        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        15.35        12.59        13.25        12.62 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.49        12.59        22.39        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP 
       13.22         4.47        25.25        13.18        13.38        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP 
       12.85        12.26         5.16        20.38        15.35        27.09 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7D 
       12.43        18.31        33.70        18.18        18.05         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       15.91        25.08        41.23         1.32         2.66 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.30 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            83.24            122.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           12.725            13.250 
[1] "0.1 - 83.2 (12.7)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         0        1        3        1        15        13
  9Q LOSS WILD-TYPE       8        4        3        0        32        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           6          7          3          2        1
  9Q LOSS WILD-TYPE        19          7          6          5        4
                   vv
clus                STAGE IVA
  9Q LOSS MUTATED           4
  9Q LOSS WILD-TYPE         0
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 1                 4
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               15                32
  STAGE IIB               13                18
  STAGE III                6                19
  STAGE IIIA               7                 7
  STAGE IIIB               3                 6
  STAGE IIIC               2                 5
  STAGE IV                 1                 4
  STAGE IVA                4                 0
[1] 12  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                T0+T1 T2 T3 T4
  9Q LOSS MUTATED       9 18 30  2
  9Q LOSS WILD-TYPE    23 25 57  3
D59V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1               9                23
  T2                 18                25
  T3                 30                57
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9Q LOSS MUTATED   25 26  4  3
  9Q LOSS WILD-TYPE 52 42  8  5
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              25                52
  N1              26                42
  N2               4                 8
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   44  5
  9Q LOSS WILD-TYPE 91  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     44    5
  9Q LOSS WILD-TYPE   91    4
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              44                91
  1               5                 4
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    7 58
  9Q LOSS WILD-TYPE 20 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      7   58
  9Q LOSS WILD-TYPE   20   99
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               7                20
  MALE                58                99
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   45 16
  9Q LOSS WILD-TYPE 79 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     45   16
  9Q LOSS WILD-TYPE   79   26
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               45                79
  YES              16                26
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   28 37
  9Q LOSS WILD-TYPE 60 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     28   37
  9Q LOSS WILD-TYPE   60   59
                                   clus
vv                                  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  28                60
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              37                59
[1] 2 2
[1] FALSE
D59V11, continuous
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED   49  3  0  2
  9Q LOSS WILD-TYPE 88  9  2  5
D59V12, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              49                88
  R1               3                 9
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED      19                         2    37
  9Q LOSS WILD-TYPE    27                         3    77
D59V14, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                  19                27
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  37                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V15, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    4 37
  9Q LOSS WILD-TYPE  2 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4   37
  9Q LOSS WILD-TYPE    2   51
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 2
  NOT HISPANIC OR LATINO              37                51
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   30 19
  10P LOSS WILD-TYPE 77 57
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                49                134 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                19                 57 
$`10P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-JY-A93C TCGA-L5-A43M TCGA-L5-A4OE 
       25.78        14.30         5.92        23.18         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NS TCGA-L5-A8NT 
        4.70         3.32         4.90         7.13        13.41        27.12 
TCGA-L5-A8NU TCGA-Q9-A6FW TCGA-V5-A7RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A50L 
       83.24         7.82        16.44        33.27         0.85         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A8NK 
        0.79        23.41        14.50         0.30         4.31        13.55 
TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       10.85        12.66        13.41        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
        4.47        25.25        12.00        13.18        13.38         0.13 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EW TCGA-VR-A8EX 
       12.85        12.26         3.42        27.09         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.18        18.05        11.24        25.08        14.37         3.42 
TCGA-Z6-AAPN 
        2.66 

$`10P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 
        4.21        32.45         7.69         3.88        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       60.39        47.38        34.85        21.70        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        3.16        30.25        18.28        26.33        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
       29.00         7.43        22.82         2.60         0.36         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NV 
       16.47        13.22         7.76         5.49         8.71        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       46.09        10.36        33.11         7.99         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         2.30        12.69         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR 
        5.29         9.27         8.98        22.82        46.19        18.21 
TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       19.73        15.68        35.21        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
       18.64         9.30        17.03        12.82         9.96         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ 
        6.28        47.93        15.48        25.12         7.40        21.37 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FP 
       12.33        10.52        12.23        12.03        13.18        12.03 
TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET 
        5.16        20.38        15.35        25.81        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       18.31        33.70        52.27         9.17        15.91        41.23 
TCGA-Z6-A8JE TCGA-Z6-A9VB 
        2.10         1.32 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.13               0.36 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             83.24             122.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             12.66              13.20 
[1] "0.1 - 83.2 (12.7)"  "0.4 - 122.1 (13.2)"
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         1        0        2        0        16         9
  10P LOSS WILD-TYPE       7        5        4        1        31        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           5          3          5          2        3
  10P LOSS WILD-TYPE        20         11          4          5        2
                    vv
clus                 STAGE IVA
  10P LOSS MUTATED           1
  10P LOSS WILD-TYPE         3
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                16                 31
  STAGE IIB                 9                 22
  STAGE III                 5                 20
  STAGE IIIA                3                 11
  STAGE IIIB                5                  4
  STAGE IIIC                2                  5
  STAGE IV                  3                  2
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  10P LOSS MUTATED       4 14 29  1
  10P LOSS WILD-TYPE    28 29 58  4
D60V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1                4                 28
  T2                  14                 29
  T3                  29                 58
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10P LOSS MUTATED   24 13  7  3
  10P LOSS WILD-TYPE 53 55  5  5
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               24                 53
  N1               13                 55
  N2                7                  5
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   41  4
  10P LOSS WILD-TYPE 94  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     41    4
  10P LOSS WILD-TYPE   94    5
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               41                 94
  1                4                  5
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     8  42
  10P LOSS WILD-TYPE  19 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8   42
  10P LOSS WILD-TYPE   19  115
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                8                 19
  MALE                 42                115
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   35  9
  10P LOSS WILD-TYPE 89 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     35    9
  10P LOSS WILD-TYPE   89   33
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                35                 89
  YES                9                 33
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   15 35
  10P LOSS WILD-TYPE 73 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     15   35
  10P LOSS WILD-TYPE   73   61
                                   clus
vv                                  10P LOSS MUTATED 10P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   15                 73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               35                 61
[1] 2 2
[1] FALSE
D60V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    34   7   1   4
  10P LOSS WILD-TYPE 103   5   1   3
D60V12, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               34                103
  R1                7                  5
  R2                1                  1
  RX                4                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED      18                         4    22
  10P LOSS WILD-TYPE    28                         1    92
D60V14, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                   18                 28
  BLACK OR AFRICAN AMERICAN                4                  1
  WHITE                                   22                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    2 26
  10P LOSS WILD-TYPE  4 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   26
  10P LOSS WILD-TYPE    4   62
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               26                 62
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   32 17
  10Q LOSS WILD-TYPE 75 59
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                134 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                17                 59 
$`10Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A4OE 
       25.78        14.30         5.92        23.18         3.16        24.00 
TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NT TCGA-L5-A8NU 
        4.70         3.32         4.90         7.13        27.12        83.24 
TCGA-V5-A7RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 
       16.44        33.27         0.85         2.63         0.53        23.41 
TCGA-IG-A97H TCGA-L5-A43H TCGA-L5-A8NK TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49R 
       14.50         0.30        13.55        10.85        12.66        13.38 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.46        12.49        22.39        12.85        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.22        12.33        25.25        12.00        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-VR-A8EP 
       13.38        13.18        12.26         5.16         3.42        27.09 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       28.11        18.18        25.08        14.37         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

$`10Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 
        4.21        32.45         7.69         3.88        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       60.39        47.38        34.85        21.70        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
       30.25        18.28         8.94        26.33        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
       29.00         7.43        22.82         2.60         0.36         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       52.57        46.09        10.36        33.11         7.82         7.99 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        7.00        20.02         5.29         9.27         8.98        22.82 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA 
       46.19        18.21        19.73        15.68        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
       20.12        18.64         9.30        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        9.96         4.67        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S 
       41.52        24.03         6.28         4.31        47.93        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       25.12         7.40        21.37         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A5U5 
       12.62        12.59        12.76        12.59        15.52         4.47 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-S8-A6BW 
       10.52        12.23         0.13        12.03        12.85        20.38 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       15.35        25.81        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-Z6-A8JD 
       41.23         3.42 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.30               0.13 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             83.24             122.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            12.660             13.235 
[1] "0.3 - 83.2 (12.7)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1"  
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         1        0        1        1        16         7
  10Q LOSS WILD-TYPE       7        5        5        0        31        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           7          5          4          2        1
  10Q LOSS WILD-TYPE        18          9          5          5        4
                    vv
clus                 STAGE IVA
  10Q LOSS MUTATED           1
  10Q LOSS WILD-TYPE         3
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                16                 31
  STAGE IIB                 7                 24
  STAGE III                 7                 18
  STAGE IIIA                5                  9
  STAGE IIIB                4                  5
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  10Q LOSS MUTATED       4 15 26  1
  10Q LOSS WILD-TYPE    28 28 61  4
D61V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                4                 28
  T2                  15                 28
  T3                  26                 61
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10Q LOSS MUTATED   21 18  4  2
  10Q LOSS WILD-TYPE 56 50  8  6
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               21                 56
  N1               18                 50
  N2                4                  8
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   43  2
  10Q LOSS WILD-TYPE 92  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     43    2
  10Q LOSS WILD-TYPE   92    7
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               43                 92
  1                2                  7
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     7  42
  10Q LOSS WILD-TYPE  20 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7   42
  10Q LOSS WILD-TYPE   20  115
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 42                115
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   32 12
  10Q LOSS WILD-TYPE 92 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     32   12
  10Q LOSS WILD-TYPE   92   30
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                32                 92
  YES               12                 30
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   13 36
  10Q LOSS WILD-TYPE 75 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     13   36
  10Q LOSS WILD-TYPE   75   60
                                   clus
vv                                  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   13                 75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               36                 60
[1] 2 2
[1] FALSE
D61V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    35   7   0   3
  10Q LOSS WILD-TYPE 102   5   2   4
D61V12, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               35                102
  R1                7                  5
  R2                0                  2
  RX                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED      20                         4    20
  10Q LOSS WILD-TYPE    26                         1    94
D61V14, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                   20                 26
  BLACK OR AFRICAN AMERICAN                4                  1
  WHITE                                   20                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    2 30
  10Q LOSS WILD-TYPE  4 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   30
  10Q LOSS WILD-TYPE    4   58
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               30                 58
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   36 16
  11P LOSS WILD-TYPE 71 60
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                52                131 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                16                 60 
$`11P LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-JY-A938 TCGA-L5-A43C 
       31.27        14.30         5.92         4.21        34.85         3.16 
TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88V TCGA-L5-A88Y 
        4.70         3.32         7.17         3.16         2.60         0.36 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L7-A6VZ TCGA-R6-A6KZ 
        3.02        55.50        16.47        13.22        10.36         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE 
       38.40         6.35         2.89         2.30        12.69        16.44 
TCGA-V5-AASW TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-L5-A43H TCGA-L5-A88S TCGA-L5-A8NK 
        9.27         0.85         2.63         0.30        15.48        13.55 
TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.85        10.45        12.66        12.43        13.41        13.38 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 
       13.25        12.59        12.49        12.76        12.85        12.33 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-VR-A8EO TCGA-VR-A8ER 
       12.03        13.18         0.13        12.85        25.81        12.43 
TCGA-VR-A8EX TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       28.11        25.08        14.37         2.10 

$`11P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB 
       32.45         7.69         3.88        14.86       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E 
       47.38        21.70        23.18        31.56        25.22        30.25 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
       18.28         8.94        24.00        26.33        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       21.01        18.35         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG 
        7.13         7.43        22.82         3.75         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       12.92        13.48         7.76         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW 
       27.12        83.24        52.57        46.09        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.99         7.59        16.31         7.04        53.95         9.30 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASX TCGA-VR-A8EQ 
       15.78         7.00        20.02         5.29         8.98        22.82 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       46.19        18.21        19.73        15.68        33.27        35.21 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ 
        6.28         4.31        47.93        25.12         7.40        21.37 
TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
        5.92        12.33        13.15        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.46        12.59        22.39        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW 
       13.18        13.38        12.03        12.26         5.16        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        3.42        15.35        27.09         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       15.91        41.23         3.42         1.32         2.66 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.13               0.53 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              55.5              122.1 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             12.43              14.86 
[1] "0.1 - 55.5 (12.4)"  "0.5 - 122.1 (14.9)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         2        2        2        1        10         7
  11P LOSS WILD-TYPE       6        3        4        0        37        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED          12          3          0          2        0
  11P LOSS WILD-TYPE        13         11          9          5        5
                    vv
clus                 STAGE IVA
  11P LOSS MUTATED           1
  11P LOSS WILD-TYPE         3
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  2                  3
  STAGE IB                  2                  4
  STAGE II                  1                  0
  STAGE IIA                10                 37
  STAGE IIB                 7                 24
  STAGE III                12                 13
  STAGE IIIA                3                 11
  STAGE IIIB                0                  9
  STAGE IIIC                2                  5
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  11P LOSS MUTATED       9  9 23  2
  11P LOSS WILD-TYPE    23 34 64  3
D62V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1                9                 23
  T2                   9                 34
  T3                  23                 64
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11P LOSS MUTATED   20 21  0  2
  11P LOSS WILD-TYPE 57 47 12  6
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               20                 57
  N1               21                 47
  N2                0                 12
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   36  1
  11P LOSS WILD-TYPE 99  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     36    1
  11P LOSS WILD-TYPE   99    8
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               36                 99
  1                1                  8
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5  47
  11P LOSS WILD-TYPE  22 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5   47
  11P LOSS WILD-TYPE   22  110
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                5                 22
  MALE                 47                110
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   29 17
  11P LOSS WILD-TYPE 95 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     29   17
  11P LOSS WILD-TYPE   95   25
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                29                 95
  YES               17                 25
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   25 27
  11P LOSS WILD-TYPE 63 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     25   27
  11P LOSS WILD-TYPE   63   69
                                   clus
vv                                  11P LOSS MUTATED 11P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   25                 63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               27                 69
[1] 2 2
[1] FALSE
D62V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    37   4   0   1
  11P LOSS WILD-TYPE 100   8   2   6
D62V12, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               37                100
  R1                4                  8
  R2                0                  2
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED      15                         3    28
  11P LOSS WILD-TYPE    31                         2    86
D62V14, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                   15                 31
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   28                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V15, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    3 26
  11P LOSS WILD-TYPE  3 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3   26
  11P LOSS WILD-TYPE    3   62
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  3
  NOT HISPANIC OR LATINO               26                 62
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   36 22
  11Q LOSS WILD-TYPE 71 54
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                58                125 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 54 
$`11Q LOSS MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-L5-A43C TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OP 
        5.92         4.21         3.16         4.70         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NL 
        3.16         2.60         3.02        55.50         2.66        13.22 
TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC 
       27.12        10.36         5.06         6.35         2.89         2.30 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A6QS 
       12.69        20.02        20.12        18.64        23.41         9.96 
TCGA-IG-A97I TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A8NK TCGA-L7-A56G 
       12.16         0.30        47.93        15.48        13.55        10.85 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 
       10.45        12.66        13.38        12.59        13.25        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.49        12.76        12.85        15.52        12.33        25.25 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-V5-A7RC TCGA-VR-A8EO 
       12.03        13.18         0.13        12.85         3.42        25.81 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7D TCGA-VR-AA7I 
       12.43        18.31        28.11        18.18         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       25.08        41.23        14.37         2.10 

$`11Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP 
        8.94        16.24        32.45         7.69         3.88        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       31.56        25.22        30.25        18.28         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
       26.33        32.61        19.99        21.01        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
       58.59         4.90        29.00         7.13         7.43        22.82 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        0.36         3.75        35.97        12.92        13.48        16.47 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       46.09        33.11         7.82         7.99         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO 
        7.04        38.40        53.95         9.30        15.78         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
        5.29        16.44         9.27         8.98        22.82        46.19 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       18.21        19.73        15.68        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.78         2.63         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       12.82         4.67        14.50        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A88W TCGA-L5-A88Z 
       41.52        24.03         6.28         4.31        25.12         7.40 
TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       21.37         5.92        12.43        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 
       15.35        12.62        12.46        12.59        22.39        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33        13.22         4.47        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW 
       13.18        13.38        12.03        12.26         5.16        20.38 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 
       15.35        27.09         1.55         8.12        33.70        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.05        11.24         3.42         1.32         2.66 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.13               0.36 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              55.5              122.1 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             12.59              13.48 
[1] "0.1 - 55.5 (12.6)"  "0.4 - 122.1 (13.5)"
[1] "hr=" "1.3"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         2        3        1        1        14         8
  11Q LOSS WILD-TYPE       6        2        5        0        33        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED          11          3          0          4        1
  11Q LOSS WILD-TYPE        14         11          9          3        4
                    vv
clus                 STAGE IVA
  11Q LOSS MUTATED           2
  11Q LOSS WILD-TYPE         2
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  3                  2
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                14                 33
  STAGE IIB                 8                 23
  STAGE III                11                 14
  STAGE IIIA                3                 11
  STAGE IIIB                0                  9
  STAGE IIIC                4                  3
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  11Q LOSS MUTATED       9 14 25  2
  11Q LOSS WILD-TYPE    23 29 62  3
D63V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1                9                 23
  T2                  14                 29
  T3                  25                 62
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11Q LOSS MUTATED   25 21  0  4
  11Q LOSS WILD-TYPE 52 47 12  4
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               25                 52
  N1               21                 47
  N2                0                 12
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   40  3
  11Q LOSS WILD-TYPE 95  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     40    3
  11Q LOSS WILD-TYPE   95    6
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               40                 95
  1                3                  6
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     8  50
  11Q LOSS WILD-TYPE  19 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8   50
  11Q LOSS WILD-TYPE   19  107
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                8                 19
  MALE                 50                107
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   33 20
  11Q LOSS WILD-TYPE 91 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     33   20
  11Q LOSS WILD-TYPE   91   22
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                33                 91
  YES               20                 22
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   20 38
  11Q LOSS WILD-TYPE 68 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     20   38
  11Q LOSS WILD-TYPE   68   58
                                   clus
vv                                  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   20                 68
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               38                 58
[1] 2 2
[1] FALSE
D63V11, continuous
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED   40  5  1  1
  11Q LOSS WILD-TYPE 97  7  1  6
D63V12, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               40                 97
  R1                5                  7
  R2                1                  1
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED      16                         4    33
  11Q LOSS WILD-TYPE    30                         1    81
D63V14, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                   16                 30
  BLACK OR AFRICAN AMERICAN                4                  1
  WHITE                                   33                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V15, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    4 29
  11Q LOSS WILD-TYPE  2 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4   29
  11Q LOSS WILD-TYPE    2   59
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               29                 59
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   20 13
  12P LOSS WILD-TYPE 87 63
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                150 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                13                 63 
$`12P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A4QS TCGA-JY-A6FH 
       25.78        31.27        13.94        32.45         3.88        47.38 
TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OP 
       34.85        25.22        30.25         8.94        32.61         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        1.38        58.59         7.13         3.75         3.02        55.50 
TCGA-L5-A8NH TCGA-L5-A8NV TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-S8-A6BV TCGA-X8-AAAR 
       12.92        52.57         7.82         5.06        20.02        18.21 
TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A5B8 TCGA-IG-A97H TCGA-LN-A49M TCGA-LN-A7HY 
       19.73        33.27         0.79        14.50        12.66        12.03 
TCGA-LN-A9FQ TCGA-V5-A7RC TCGA-Z6-A8JE 
       12.85         3.42         2.10 

$`12P LOSS WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A939 
        4.21         7.69        14.86       122.10        60.39        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OF 
       23.18        31.56         3.16        18.28        24.00        26.33 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
        4.70        19.99        21.01        18.35         3.32         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y 
        4.90        29.00         7.43        22.82         2.60         0.36 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        35.97        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49         8.71        13.41        27.12        83.24        46.09 
TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       10.36        33.11         7.99         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        2.30        12.69         7.00         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.98        22.82        46.19        15.68        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I 
       17.03        23.41        12.82         9.96         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        0.30         4.31        47.93        15.48        25.12         7.40 
TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       13.55        21.37        10.85         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
       12.26         5.16        20.38        15.35        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.79               0.13 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             58.59             122.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             13.94              13.00 
[1] "0.8 - 58.6 (13.9)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "1.3"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         3        1        1        0         6         7
  12P LOSS WILD-TYPE       5        4        5        1        41        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           2          4          2          1        1
  12P LOSS WILD-TYPE        23         10          7          6        4
                    vv
clus                 STAGE IVA
  12P LOSS MUTATED           0
  12P LOSS WILD-TYPE         4
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 6                 41
  STAGE IIB                 7                 24
  STAGE III                 2                 23
  STAGE IIIA                4                 10
  STAGE IIIB                2                  7
  STAGE IIIC                1                  6
  STAGE IV                  1                  4
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  12P LOSS MUTATED       8  6 17  0
  12P LOSS WILD-TYPE    24 37 70  5
D64V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                8                 24
  T2                   6                 37
  T3                  17                 70
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  12P LOSS MUTATED   12 13  4  1
  12P LOSS WILD-TYPE 65 55  8  7
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               12                 65
  N1               13                 55
  N2                4                  8
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    24   1
  12P LOSS WILD-TYPE 111   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     24    1
  12P LOSS WILD-TYPE  111    8
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               24                111
  1                1                  8
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     6  27
  12P LOSS WILD-TYPE  21 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6   27
  12P LOSS WILD-TYPE   21  130
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                6                 21
  MALE                 27                130
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   27  2
  12P LOSS WILD-TYPE 97 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     27    2
  12P LOSS WILD-TYPE   97   40
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                27                 97
  YES                2                 40
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   25  8
  12P LOSS WILD-TYPE 63 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     25    8
  12P LOSS WILD-TYPE   63   88
                                   clus
vv                                  12P LOSS MUTATED 12P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   25                 63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                8                 88
[1] 2 2
[1] FALSE
D64V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    24   3   0   3
  12P LOSS WILD-TYPE 113   9   2   4
D64V12, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               24                113
  R1                3                  9
  R2                0                  2
  RX                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       4                         1    22
  12P LOSS WILD-TYPE    42                         4    92
D64V14, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    4                 42
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   22                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    0 14
  12P LOSS WILD-TYPE  6 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   14
  12P LOSS WILD-TYPE    6   74
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               14                 74
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED   19 12
  12Q LOSS WILD-TYPE 88 64
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                152 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                12                 64 
$`12Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GM TCGA-IG-A4QS TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E 
       31.27        13.94         3.88        47.38        34.85        25.22 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW 
       30.25         8.94        32.61         7.17        58.59         7.13 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-Q9-A6FW TCGA-R6-A6KZ 
        3.02        55.50         2.66        12.92         7.82         5.06 
TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-AASX TCGA-X8-AAAR TCGA-IG-A3I8 TCGA-IG-A5B8 
        2.89        20.02         8.98        18.21        33.27         0.79 
TCGA-IG-A5S3 TCGA-IG-A97H TCGA-L7-A56G TCGA-LN-A9FQ TCGA-V5-A7RC TCGA-VR-A8ET 
       23.41        14.50        10.85        12.85         3.42         1.55 
TCGA-XP-A8T8 
       14.37 

$`12Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6F8 
       16.24         4.21        32.45         7.69        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43I 
       60.39        21.70        23.18        31.56         3.16        18.28 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       24.00        26.33         4.70        19.99        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         1.38         3.16         4.90        29.00         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NI 
       22.82         2.60         0.36         3.75        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       27.12        83.24        52.57        46.09        10.36        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.99         7.59        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30        15.78         2.30        12.69         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-ZR-A9CJ 
        5.29        16.44         9.27        22.82        46.19        19.73 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       15.68        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       18.64         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S 
       24.03         6.28         0.30         4.31        47.93        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49L 
       25.12         7.40        13.55        21.37         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW 
       13.18         0.13        12.03        12.26         5.16        20.38 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       15.35        25.81        27.09        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        15.91        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.79               0.13 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             58.59             122.10 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            12.920             13.165 
[1] "0.8 - 58.6 (12.9)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         3        1        1        0         4         9
  12Q LOSS WILD-TYPE       5        4        5        1        43        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0          2          2          0        1
  12Q LOSS WILD-TYPE        25         12          7          7        4
                    vv
clus                 STAGE IVA
  12Q LOSS MUTATED           1
  12Q LOSS WILD-TYPE         3
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 4                 43
  STAGE IIB                 9                 22
  STAGE III                 0                 25
  STAGE IIIA                2                 12
  STAGE IIIB                2                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  12Q LOSS MUTATED      10  5 11  0
  12Q LOSS WILD-TYPE    22 38 76  5
D65V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               10                 22
  T2                   5                 38
  T3                  11                 76
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  12Q LOSS MUTATED   12 10  3  0
  12Q LOSS WILD-TYPE 65 58  9  8
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               12                 65
  N1               10                 58
  N2                3                  9
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    20   2
  12Q LOSS WILD-TYPE 115   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     20    2
  12Q LOSS WILD-TYPE  115    7
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               20                115
  1                2                  7
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     7  24
  12Q LOSS WILD-TYPE  20 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      7   24
  12Q LOSS WILD-TYPE   20  133
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 24                133
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    24   3
  12Q LOSS WILD-TYPE 100  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     24    3
  12Q LOSS WILD-TYPE  100   39
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                24                100
  YES                3                 39
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   22  9
  12Q LOSS WILD-TYPE 66 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     22    9
  12Q LOSS WILD-TYPE   66   87
                                   clus
vv                                  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   22                 66
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                9                 87
[1] 2 2
[1] FALSE
D65V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    21   1   0   2
  12Q LOSS WILD-TYPE 116  11   2   5
D65V12, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               21                116
  R1                1                 11
  R2                0                  2
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       2                         3    22
  12Q LOSS WILD-TYPE    44                         2    92
D65V14, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    2                 44
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   22                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V15, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    1 14
  12Q LOSS WILD-TYPE  5 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   14
  12Q LOSS WILD-TYPE    5   74
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               14                 74
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   40 26
  13Q LOSS WILD-TYPE 67 50
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                66                117 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                26                 50 
$`13Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE 
       25.78        58.55         7.63         8.94        32.45         7.69 
TCGA-IG-A4QS TCGA-JY-A6FB TCGA-JY-A93E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ 
        3.88        60.39        25.22        24.00        26.33        21.01 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A891 TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS 
        3.16        29.00         3.75        13.22         5.49        13.41 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WG 
       83.24        10.36         5.06        38.40         6.35        12.69 
TCGA-VR-A8EQ TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A50L TCGA-IG-A51D 
       22.82        35.21         0.85        20.78         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FD TCGA-L5-A4OM TCGA-L7-A56G 
       23.41         9.96        44.75        68.02        47.93        10.85 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        13.41        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       15.35        13.25        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       12.85        13.22        12.33        10.52        12.23        12.03 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FR TCGA-VR-A8EO TCGA-VR-A8EP 
       13.38        13.18         0.13        12.26        25.81        27.09 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-XP-A8T8 
       18.31        28.11        18.18        52.27        15.91        14.37 

$`13Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       14.86       122.10        47.38        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       31.56         3.16        30.25        18.28         8.94         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        19.99        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
       58.59         4.90         7.13         7.43        22.82         2.60 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NV 
       13.48        16.47         7.76         8.71        27.12        52.57 
TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       46.09        33.11         7.82         7.99         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04        53.95         9.30        15.78         2.89         2.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.02         5.29        16.44         9.27         8.98 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YB 
       46.19        18.21        19.73        15.68        33.27         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 
       20.12        18.64         9.30         0.79        12.82         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       14.50        12.16         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK 
        0.30         4.31        15.48        25.12         7.40        13.55 
TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       21.37        12.66        12.33        12.59        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59        15.52        11.54        12.33         4.47        25.25 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FU TCGA-S8-A6BW 
       12.00        13.18        12.03        12.85         5.16        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY 
        3.42        15.35        12.43         1.55         8.12        33.70 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
       18.05        11.24         9.17        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        2.10         1.32         2.66 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.13               0.30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             83.24             122.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            13.315             12.620 
[1] "0.1 - 83.2 (13.3)"  "0.3 - 122.1 (12.6)"
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         3        2        0        1        20        11
  13Q LOSS WILD-TYPE       5        3        6        0        27        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED          12          5          3          2        1
  13Q LOSS WILD-TYPE        13          9          6          5        4
                    vv
clus                 STAGE IVA
  13Q LOSS MUTATED           1
  13Q LOSS WILD-TYPE         3
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  2                  3
  STAGE IB                  0                  6
  STAGE II                  1                  0
  STAGE IIA                20                 27
  STAGE IIB                11                 20
  STAGE III                12                 13
  STAGE IIIA                5                  9
  STAGE IIIB                3                  6
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  13Q LOSS MUTATED      11 17 31  3
  13Q LOSS WILD-TYPE    21 26 56  2
D66V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               11                 21
  T2                  17                 26
  T3                  31                 56
  T4                   3                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  13Q LOSS MUTATED   31 26  3  2
  13Q LOSS WILD-TYPE 46 42  9  6
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               31                 46
  N1               26                 42
  N2                3                  9
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   55  2
  13Q LOSS WILD-TYPE 80  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     55    2
  13Q LOSS WILD-TYPE   80    7
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               55                 80
  1                2                  7
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    5 62
  13Q LOSS WILD-TYPE 22 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5   62
  13Q LOSS WILD-TYPE   22   95
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                5                 22
  MALE                 62                 95
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   42 21
  13Q LOSS WILD-TYPE 82 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     42   21
  13Q LOSS WILD-TYPE   82   21
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                42                 82
  YES               21                 21
[1] 2 2
[1] FALSE
D66V9, continuous
D66V10, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   25 42
  13Q LOSS WILD-TYPE 63 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     25   42
  13Q LOSS WILD-TYPE   63   54
                                   clus
vv                                  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   25                 63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               42                 54
[1] 2 2
[1] FALSE
D66V11, continuous
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED   53  2  1  2
  13Q LOSS WILD-TYPE 84 10  1  5
D66V12, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               53                 84
  R1                2                 10
  R2                1                  1
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED      26                         2    33
  13Q LOSS WILD-TYPE    20                         3    81
D66V14, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                   26                 20
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                   33                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2 36
  13Q LOSS WILD-TYPE  4 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   36
  13Q LOSS WILD-TYPE    4   52
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               36                 52
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   23 22
  14Q LOSS WILD-TYPE 84 54
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                138 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                22                 54 
$`14Q LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-JY-A6F8 
        7.63         8.94        16.24         4.21        32.45       122.10 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        47.38        25.22        18.28         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A891 
       26.33         4.70        32.61         7.13         0.36         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DQ 
       55.50         2.66        16.47        10.36        33.11         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-VR-A8EQ 
        5.06         6.35         9.30        15.78         7.00        22.82 
TCGA-IG-A3QL TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-L5-A43H 
       35.21        23.41        12.82         4.67        14.50         0.30 
TCGA-L5-A88S TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49W TCGA-LN-A7HV TCGA-VR-A8EO 
       15.48        10.85        10.45        13.25        10.52        25.81 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-Z6-AAPN 
       52.27        18.05         2.66 

$`14Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        7.69         3.88        14.86        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       31.56         3.16        30.25        19.99        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NG 
       29.00         7.43        22.82         2.60         3.02        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       12.92        13.48        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-Q9-A6FW 
       13.41        27.12        83.24        52.57        46.09         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 
        7.99        16.31         7.04        38.40        53.95         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        2.30        12.69        20.02         5.29        16.44         9.27 
TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 
        8.98        46.19        18.21        19.73        15.68        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FA 
        0.53        17.03         0.79         9.96        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J 
       68.02         3.68        41.52        24.03         6.28         4.31 
TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K 
       47.93        25.12         7.40        13.55        21.37         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC 
       12.03        12.85        12.26         5.16        20.38         3.42 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       15.35        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       28.11        33.70        18.18        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.30               0.13 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            122.10              83.24 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            13.250             13.035 
[1] "0.3 - 122.1 (13.2)" "0.1 - 83.2 (13.0)" 
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         4        0        1        0         8         6
  14Q LOSS WILD-TYPE       4        5        5        1        39        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           7          4          3          1        0
  14Q LOSS WILD-TYPE        18         10          6          6        5
                    vv
clus                 STAGE IVA
  14Q LOSS MUTATED           3
  14Q LOSS WILD-TYPE         1
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  0                  5
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 8                 39
  STAGE IIB                 6                 25
  STAGE III                 7                 18
  STAGE IIIA                4                 10
  STAGE IIIB                3                  6
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 3                  1
[1] 12  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                 T0+T1 T2 T3 T4
  14Q LOSS MUTATED       8  7 25  0
  14Q LOSS WILD-TYPE    24 36 62  5
D67V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1                8                 24
  T2                   7                 36
  T3                  25                 62
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  14Q LOSS MUTATED   15 18  5  1
  14Q LOSS WILD-TYPE 62 50  7  7
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               15                 62
  N1               18                 50
  N2                5                  7
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    30   3
  14Q LOSS WILD-TYPE 105   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     30    3
  14Q LOSS WILD-TYPE  105    6
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               30                105
  1                3                  6
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     7  38
  14Q LOSS WILD-TYPE  20 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      7   38
  14Q LOSS WILD-TYPE   20  119
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 38                119
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   31  8
  14Q LOSS WILD-TYPE 93 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     31    8
  14Q LOSS WILD-TYPE   93   34
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                31                 93
  YES                8                 34
[1] 2 2
[1] FALSE
D67V9, continuous
D67V10, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   30 15
  14Q LOSS WILD-TYPE 58 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     30   15
  14Q LOSS WILD-TYPE   58   81
                                   clus
vv                                  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   30                 58
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               15                 81
[1] 2 2
[1] FALSE
D67V11, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    30   4   0   2
  14Q LOSS WILD-TYPE 107   8   2   5
D67V12, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               30                107
  R1                4                  8
  R2                0                  2
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       6                         1    30
  14Q LOSS WILD-TYPE    40                         4    84
D67V14, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    6                 40
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   30                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V15, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    1 15
  14Q LOSS WILD-TYPE  5 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   15
  14Q LOSS WILD-TYPE    5   73
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               15                 73
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   35 22
  15Q LOSS WILD-TYPE 72 54
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                57                126 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                 54 
$`15Q LOSS MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A938 
        5.92        16.24        32.45         7.69         3.88        34.85 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       23.18        31.56        25.22        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NE 
        4.70        32.61         4.90        29.00         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NR 
        2.66        35.97        12.92        13.48         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-RE-A7BO 
       13.41        27.12        83.24         5.06        38.40         7.00 
TCGA-S8-A6BV TCGA-V5-A7RE TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IG-A3QL TCGA-IG-A3YC 
       20.02        16.44        18.21        19.73        35.21        20.12 
TCGA-IG-A4P3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-L5-A43H TCGA-L5-A4OM TCGA-LN-A4A1 
       18.64         4.67        14.50         0.30        47.93        12.59 
TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A8I0 
       22.39        12.33        12.33        25.25        12.03        13.38 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-VR-A8EO TCGA-VR-A8EU TCGA-XP-A8T6 
       12.03        12.85        12.26        25.81        18.31        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN 
       14.37         2.10         2.66 

$`15Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
        8.94         4.21        14.86       122.10        60.39        47.38 
TCGA-JY-A939 TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ 
       21.70         3.16        30.25        26.33        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
        7.13         7.43        22.82         2.60         0.36         3.75 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       16.47        13.22         7.76        52.57        46.09        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         7.99         7.59        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
       12.69         5.29         9.27         8.98        22.82        46.19 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT 
       15.68        33.27         0.85        20.78         2.63         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK 
        6.28         4.31        15.48        25.12         7.40        13.55 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       12.85        15.52        11.54        13.22         4.47        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-Q9-A6FU 
       12.00        12.23        13.18        13.18         0.13         5.16 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
       20.38         3.42        15.35        27.09        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       11.24         9.17        15.91        41.23         3.42         1.32 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.30               0.13 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             83.24             122.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            14.500             12.675 
[1] "0.3 - 83.2 (14.5)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.3"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         3        1        1        0        13        11
  15Q LOSS WILD-TYPE       5        4        5        1        34        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           8          5          4          2        3
  15Q LOSS WILD-TYPE        17          9          5          5        2
                    vv
clus                 STAGE IVA
  15Q LOSS MUTATED           2
  15Q LOSS WILD-TYPE         2
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                13                 34
  STAGE IIB                11                 20
  STAGE III                 8                 17
  STAGE IIIA                5                  9
  STAGE IIIB                4                  5
  STAGE IIIC                2                  5
  STAGE IV                  3                  2
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  15Q LOSS MUTATED      12 12 31  0
  15Q LOSS WILD-TYPE    20 31 56  5
D68V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1               12                 20
  T2                  12                 31
  T3                  31                 56
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  15Q LOSS MUTATED   22 25  5  2
  15Q LOSS WILD-TYPE 55 43  7  6
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               22                 55
  N1               25                 43
  N2                5                  7
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   43  5
  15Q LOSS WILD-TYPE 92  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     43    5
  15Q LOSS WILD-TYPE   92    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               43                 92
  1                5                  4
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7  50
  15Q LOSS WILD-TYPE  20 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7   50
  15Q LOSS WILD-TYPE   20  107
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 50                107
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   41 12
  15Q LOSS WILD-TYPE 83 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     41   12
  15Q LOSS WILD-TYPE   83   30
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                41                 83
  YES               12                 30
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   34 23
  15Q LOSS WILD-TYPE 54 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     34   23
  15Q LOSS WILD-TYPE   54   73
                                   clus
vv                                  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   34                 54
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               23                 73
[1] 2 2
[1] FALSE
D68V11, continuous
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   43  7  0  3
  15Q LOSS WILD-TYPE 94  5  2  4
D68V12, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               43                 94
  R1                7                  5
  R2                0                  2
  RX                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED      13                         2    37
  15Q LOSS WILD-TYPE    33                         3    77
D68V14, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                   13                 33
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                   37                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V15, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    2 26
  15Q LOSS WILD-TYPE  4 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   26
  15Q LOSS WILD-TYPE    4   62
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               26                 62
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   29 25
  16P LOSS WILD-TYPE 78 51
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                54                129 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                25                 51 
$`16P LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-JY-A6FH 
        7.63         5.92        13.94         8.94        32.45        47.38 
TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A4OE 
       34.85        23.18        25.22         3.16        18.28        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        4.70        32.61        21.01         3.16        58.59         4.90 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NU 
        0.36         3.75         3.02        12.92         5.49        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-R6-A6DN TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       52.57        46.09         7.99         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         2.30        12.69         7.00         5.29        16.44 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-IG-A3YC TCGA-L5-A88Z TCGA-LN-A49L TCGA-LN-A49N 
        9.27        22.82        20.12         7.40        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A7HW TCGA-LN-A9FR 
       13.41        12.59        22.39        12.33        12.00        12.26 
TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8Q7 TCGA-Z6-A8JE TCGA-Z6-AAPN 
        5.16         3.42        27.09        52.27         2.10         2.66 

$`16P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30        58.55        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A939 
        7.69         3.88        14.86       122.10        60.39        21.70 
TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON 
       31.56        30.25         8.94        26.33        19.99        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         7.17         1.38        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI 
       22.82         2.60        55.50         2.66        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       16.47        13.22         7.76         8.71        13.41        27.12 
TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       10.36        33.11         7.82         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-AASX TCGA-VR-AA4D 
        7.04        38.40        15.78        20.02         8.98        46.19 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       18.21        19.73        15.68        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
        6.28         0.30         4.31        47.93        15.48        25.12 
TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49P 
       13.55        21.37        10.85         5.92        12.66        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        15.35        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER 
       12.03        12.85        20.38        15.35        25.81        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       14.37         3.42         1.32 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.36               0.13 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             83.24             122.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            12.295             13.250 
[1] "0.4 - 83.2 (12.3)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         4        1        2        0        10         7
  16P LOSS WILD-TYPE       4        4        4        1        37        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           6          5          4          0        2
  16P LOSS WILD-TYPE        19          9          5          7        3
                    vv
clus                 STAGE IVA
  16P LOSS MUTATED           0
  16P LOSS WILD-TYPE         4
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  4
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                10                 37
  STAGE IIB                 7                 24
  STAGE III                 6                 19
  STAGE IIIA                5                  9
  STAGE IIIB                4                  5
  STAGE IIIC                0                  7
  STAGE IV                  2                  3
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  16P LOSS MUTATED      12  9 23  0
  16P LOSS WILD-TYPE    20 34 64  5
D69V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1               12                 20
  T2                   9                 34
  T3                  23                 64
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16P LOSS MUTATED   18 22  4  0
  16P LOSS WILD-TYPE 59 46  8  8
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               18                 59
  N1               22                 46
  N2                4                  8
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   37  2
  16P LOSS WILD-TYPE 98  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     37    2
  16P LOSS WILD-TYPE   98    7
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               37                 98
  1                2                  7
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7  47
  16P LOSS WILD-TYPE  20 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7   47
  16P LOSS WILD-TYPE   20  110
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 47                110
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   39  9
  16P LOSS WILD-TYPE 85 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     39    9
  16P LOSS WILD-TYPE   85   33
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                39                 85
  YES                9                 33
[1] 2 2
[1] FALSE
D69V9, continuous
D69V10, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   38 16
  16P LOSS WILD-TYPE 50 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     38   16
  16P LOSS WILD-TYPE   50   80
                                   clus
vv                                  16P LOSS MUTATED 16P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   38                 50
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               16                 80
[1] 2 2
[1] FALSE
D69V11, continuous
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED   38  4  0  3
  16P LOSS WILD-TYPE 99  8  2  4
D69V12, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               38                 99
  R1                4                  8
  R2                0                  2
  RX                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       9                         1    38
  16P LOSS WILD-TYPE    37                         4    76
D69V14, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    9                 37
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   38                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3 21
  16P LOSS WILD-TYPE  3 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   21
  16P LOSS WILD-TYPE    3   67
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  3
  NOT HISPANIC OR LATINO               21                 67
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   29 24
  16Q LOSS WILD-TYPE 78 52
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                130 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                24                 52 
$`16Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       31.27         7.63         5.92         8.94        16.24        32.45 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A43M 
       47.38        34.85        23.18         3.16        18.28         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OS 
       24.00         4.70        32.61        21.01         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NN 
        4.90         0.36         3.75         3.02        55.50         5.49 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-R6-A6KZ TCGA-R6-A6XQ 
        8.71        83.24        46.09        10.36         5.06         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EQ TCGA-IG-A3QL TCGA-IG-A3YC 
        5.29        16.44         9.27        22.82        35.21        20.12 
TCGA-IG-A97H TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4MQ 
       14.50        10.85        10.45        13.41        12.59        12.33 
TCGA-LN-A7HV TCGA-Q9-A6FU TCGA-VR-A8EP TCGA-XP-A8T6 TCGA-Z6-AAPN 
       10.52         5.16        27.09        25.08         2.66 

$`16Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       25.78        14.30        58.55        13.94         4.21         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93D 
        3.88        14.86       122.10        60.39        21.70        31.56 
TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO 
       25.22        30.25        26.33        19.99        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        7.17         1.38        29.00         7.13         7.43        22.82 
TCGA-L5-A88V TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        2.60         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-M9-A5M8 
       13.22         7.76        13.41        27.12        52.57        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         7.99         7.59        16.31         7.04        38.40 
TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ 
       15.78        20.02         8.98        46.19        18.21        19.73 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 
       15.68        33.27         0.85        20.78         2.63        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        9.96         4.67        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM 
       41.52        24.03         6.28         0.30         4.31        47.93 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K 
       15.48        25.12         7.40        13.55        21.37         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        12.33        13.38        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.59        22.39        12.85        15.52        11.54        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        25.25        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER 
       12.26        20.38         3.42        15.35        25.81        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       52.27        18.05        11.24         9.17        15.91        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       14.37         3.42         2.10         1.32 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.36               0.13 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             83.24             122.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             10.85              13.22 
[1] "0.4 - 83.2 (10.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         4        1        2        0         9         7
  16Q LOSS WILD-TYPE       4        4        4        1        38        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           7          2          4          1        1
  16Q LOSS WILD-TYPE        18         12          5          6        4
                    vv
clus                 STAGE IVA
  16Q LOSS MUTATED           1
  16Q LOSS WILD-TYPE         3
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  4
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                 9                 38
  STAGE IIB                 7                 24
  STAGE III                 7                 18
  STAGE IIIA                2                 12
  STAGE IIIB                4                  5
  STAGE IIIC                1                  6
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  16Q LOSS MUTATED      10  9 24  0
  16Q LOSS WILD-TYPE    22 34 63  5
D70V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               10                 22
  T2                   9                 34
  T3                  24                 63
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16Q LOSS MUTATED   16 20  5  1
  16Q LOSS WILD-TYPE 61 48  7  7
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               16                 61
  N1               20                 48
  N2                5                  7
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    34   2
  16Q LOSS WILD-TYPE 101   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     34    2
  16Q LOSS WILD-TYPE  101    7
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               34                101
  1                2                  7
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     8  45
  16Q LOSS WILD-TYPE  19 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8   45
  16Q LOSS WILD-TYPE   19  112
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                8                 19
  MALE                 45                112
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   38 10
  16Q LOSS WILD-TYPE 86 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     38   10
  16Q LOSS WILD-TYPE   86   32
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                38                 86
  YES               10                 32
[1] 2 2
[1] FALSE
D70V9, continuous
D70V10, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   40 13
  16Q LOSS WILD-TYPE 48 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     40   13
  16Q LOSS WILD-TYPE   48   83
                                   clus
vv                                  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   40                 48
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               13                 83
[1] 2 2
[1] FALSE
D70V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    36   5   0   3
  16Q LOSS WILD-TYPE 101   7   2   4
D70V12, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               36                101
  R1                5                  7
  R2                0                  2
  RX                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       7                         2    35
  16Q LOSS WILD-TYPE    39                         3    79
D70V14, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    7                 39
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                   35                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V15, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4 20
  16Q LOSS WILD-TYPE  2 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4   20
  16Q LOSS WILD-TYPE    2   68
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               20                 68
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   40 30
  17P LOSS WILD-TYPE 67 46
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                70                113 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                30                 46 
$`17P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78         7.63         5.92         8.94         4.21        32.45 
TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43E 
        3.88       122.10        47.38        34.85        31.56        30.25 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP 
       24.00        26.33         4.70        32.61         3.32         7.17 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
        4.90         7.13         7.43         2.60         0.36         3.75 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       16.47        13.22         5.49         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG 
       83.24        33.11         7.82         7.59         7.04        38.40 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         2.30        12.69         7.00        20.02 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-X8-AAAR TCGA-IG-A4P3 
       16.44         9.27         8.98        22.82        18.21        18.64 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S 
        0.79        23.41        14.50         5.92        10.45        13.15 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-Q9-A6FU 
       13.25        12.59        12.33        10.52        13.18         5.16 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 
       15.35        27.09        12.43         8.12        18.18        52.27 
TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       11.24        25.08        14.37         2.66 

$`17P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE 
       31.27        14.30        58.55        13.94        16.24         7.69 
TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C 
       14.86        60.39        21.70        23.18        25.22         3.16 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
       18.28         8.94        19.99        21.01        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A893 TCGA-L5-A8NE 
        3.16        58.59        29.00        22.82         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NV 
        2.66        35.97        12.92        13.48         7.76        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ 
       46.09        10.36         7.99         5.06        16.31         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RB TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IC-A6RF 
       53.95         2.89         5.29        46.19        19.73        15.68 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        9.30         0.53        17.03        12.82         9.96         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
        6.28         0.30         4.31        47.93        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49N 
        7.40        13.55        21.37        10.85        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       13.41        12.33        13.38        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.00        12.23        12.03        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO 
       12.03        12.85        12.26        20.38         3.42        25.81 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7D 
        1.55        18.31        28.11        33.70        18.05         9.17 
TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        41.23         3.42         2.10         1.32 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.36               0.13 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            122.10              68.02 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             12.64              13.22 
[1] "0.4 - 122.1 (12.6)" "0.1 - 68.0 (13.2)" 
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         4        1        2        0        12        14
  17P LOSS WILD-TYPE       4        4        4        1        35        17
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED          13          2          6          3        2
  17P LOSS WILD-TYPE        12         12          3          4        3
                    vv
clus                 STAGE IVA
  17P LOSS MUTATED           1
  17P LOSS WILD-TYPE         3
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  4
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                12                 35
  STAGE IIB                14                 17
  STAGE III                13                 12
  STAGE IIIA                2                 12
  STAGE IIIB                6                  3
  STAGE IIIC                3                  4
  STAGE IV                  2                  3
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  17P LOSS MUTATED      11 12 39  1
  17P LOSS WILD-TYPE    21 31 48  4
D71V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               11                 21
  T2                  12                 31
  T3                  39                 48
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17P LOSS MUTATED   24 28  6  4
  17P LOSS WILD-TYPE 53 40  6  4
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               24                 53
  N1               28                 40
  N2                6                  6
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   52  3
  17P LOSS WILD-TYPE 83  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     52    3
  17P LOSS WILD-TYPE   83    6
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               52                 83
  1                3                  6
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    9 62
  17P LOSS WILD-TYPE 18 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      9   62
  17P LOSS WILD-TYPE   18   95
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                9                 18
  MALE                 62                 95
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   46 15
  17P LOSS WILD-TYPE 78 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     46   15
  17P LOSS WILD-TYPE   78   27
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                46                 78
  YES               15                 27
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   47 24
  17P LOSS WILD-TYPE 41 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     47   24
  17P LOSS WILD-TYPE   41   72
                                   clus
vv                                  17P LOSS MUTATED 17P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   47                 41
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               24                 72
[1] 2 2
[1] FALSE
D71V11, continuous
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   47  6  0  3
  17P LOSS WILD-TYPE 90  6  2  4
D71V12, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               47                 90
  R1                6                  6
  R2                0                  2
  RX                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED      11                         3    47
  17P LOSS WILD-TYPE    35                         2    67
D71V14, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                   11                 35
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   47                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    4 28
  17P LOSS WILD-TYPE  2 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   28
  17P LOSS WILD-TYPE    2   60
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               28                 60
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   13 12
  17Q LOSS WILD-TYPE 94 64
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                158 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 64 
$`17Q LOSS MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-JY-A938 TCGA-L5-A4OW TCGA-L5-A88Y 
        8.94         4.21         7.69        34.85         7.13         0.36 
TCGA-L5-A891 TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ 
        3.75         9.30        12.69        16.44         8.98        22.82 
TCGA-X8-AAAR TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-LN-A49L TCGA-LN-A4A1 
       18.21         0.79        23.41        14.50        10.45        12.59 
TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-VR-A8ER TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-XP-A8T6 
       12.33         5.16        12.43        28.11        52.27        25.08 
TCGA-Z6-AAPN 
        2.66 

$`17Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 
       13.94        16.24        32.45         3.88        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       60.39        47.38        21.70        23.18        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16        30.25        18.28         8.94        24.00        26.33 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        4.70        32.61        19.99        21.01        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.43        22.82         2.60         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       46.09        10.36        33.11         7.82         7.99         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.02         5.29 
TCGA-V5-AASW TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        9.27        46.19        19.73        15.68        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I 
        0.53        17.03        12.82         9.96         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02         3.68        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        0.30         4.31        47.93        15.48        25.12         7.40 
TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       13.55        21.37        10.85         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
       12.26        20.38         3.42        15.35        25.81        27.09 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G 
        1.55        18.31         8.12        33.70        18.18        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       11.24         9.17        15.91        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB 
        2.10         1.32 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.36               0.13 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             52.27             122.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             12.33              13.22 
[1] "0.4 - 52.3 (12.3)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.5"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0        0        2        0         4         6
  17Q LOSS WILD-TYPE       8        5        4        1        43        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           4          1          1          0        0
  17Q LOSS WILD-TYPE        21         13          8          7        5
                    vv
clus                 STAGE IVA
  17Q LOSS MUTATED           1
  17Q LOSS WILD-TYPE         3
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                 4                 43
  STAGE IIB                 6                 25
  STAGE III                 4                 21
  STAGE IIIA                1                 13
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  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                 T0+T1 T2 T3 T4
  17Q LOSS MUTATED       5  4 12  1
  17Q LOSS WILD-TYPE    27 39 75  4
D72V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                5                 27
  T2                   4                 39
  T3                  12                 75
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17Q LOSS MUTATED    8 12  1  0
  17Q LOSS WILD-TYPE 69 56 11  8
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                8                 69
  N1               12                 56
  N2                1                 11
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    19   1
  17Q LOSS WILD-TYPE 116   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     19    1
  17Q LOSS WILD-TYPE  116    8
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               19                116
  1                1                  8
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3  22
  17Q LOSS WILD-TYPE  24 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   22
  17Q LOSS WILD-TYPE   24  135
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                3                 24
  MALE                 22                135
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    16   5
  17Q LOSS WILD-TYPE 108  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     16    5
  17Q LOSS WILD-TYPE  108   37
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                16                108
  YES                5                 37
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   13 12
  17Q LOSS WILD-TYPE 75 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     13   12
  17Q LOSS WILD-TYPE   75   84
                                   clus
vv                                  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   13                 75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               12                 84
[1] 2 2
[1] FALSE
D72V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    17   1   0   1
  17Q LOSS WILD-TYPE 120  11   2   6
D72V12, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               17                120
  R1                1                 11
  R2                0                  2
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       4                         1    15
  17Q LOSS WILD-TYPE    42                         4    99
D72V14, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    4                 42
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   15                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3 12
  17Q LOSS WILD-TYPE  3 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   12
  17Q LOSS WILD-TYPE    3   76
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  3
  NOT HISPANIC OR LATINO               12                 76
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   41 30
  18P LOSS WILD-TYPE 66 46
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                71                112 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                30                 46 
$`18P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        14.30         5.92         8.94        16.24        32.45 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       47.38        23.18        31.56        25.22         3.16        30.25 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       18.28         8.94        24.00        26.33         4.70        32.61 
TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.17         7.43         2.60         3.75        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NV 
       35.97        12.92        13.48        16.47         8.71        52.57 
TCGA-L7-A6VZ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
       10.36         7.82         7.59        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW 
        9.30         2.30         7.00        20.02         5.29         9.27 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A5B8 
       18.21        19.73        33.27         0.85         2.63         0.79 
TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93F TCGA-L5-A43H TCGA-L5-A88S 
       23.41        14.50        44.75        24.03         0.30        15.48 
TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       13.55         5.92        10.45        12.43        13.41        12.33 
TCGA-LN-A4A1 TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-Q9-A6FU TCGA-VR-A8EP 
       12.59        12.03        13.18        12.85         5.16        27.09 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       18.31         8.12        41.23         3.42         2.66 

$`18P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        58.55         7.63        13.94         4.21         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A939 
        3.88        14.86       122.10        60.39        34.85        21.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       19.99        21.01        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88Y 
       58.59         4.90        29.00         7.13        22.82         0.36 
TCGA-L5-A893 TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NT 
        3.02        13.22         7.76         5.49        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       83.24        46.09        33.11         7.99         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASX 
        7.04        15.78         2.89        12.69        16.44         8.98 
TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
       22.82        46.19        15.68        35.21        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       18.64         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
        4.67        12.16        68.02         3.68        41.52         6.28 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L7-A56G 
        4.31        47.93        25.12         7.40        21.37        10.85 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.66        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC 
       13.38         0.13        12.03        12.26        20.38         3.42 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       15.35        25.81        12.43         1.55        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        14.37         2.10         1.32 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.30               0.13 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              55.5              122.1 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            12.920             13.165 
[1] "0.3 - 55.5 (12.9)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         3        1        3        0        14         9
  18P LOSS WILD-TYPE       5        4        3        1        33        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED          11          5          6          3        2
  18P LOSS WILD-TYPE        14          9          3          4        3
                    vv
clus                 STAGE IVA
  18P LOSS MUTATED           2
  18P LOSS WILD-TYPE         2
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  3                  3
  STAGE II                  0                  1
  STAGE IIA                14                 33
  STAGE IIB                 9                 22
  STAGE III                11                 14
  STAGE IIIA                5                  9
  STAGE IIIB                6                  3
  STAGE IIIC                3                  4
  STAGE IV                  2                  3
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  18P LOSS MUTATED      11 10 41  1
  18P LOSS WILD-TYPE    21 33 46  4
D73V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               11                 21
  T2                  10                 33
  T3                  41                 46
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18P LOSS MUTATED   25 27  7  3
  18P LOSS WILD-TYPE 52 41  5  5
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               25                 52
  N1               27                 41
  N2                7                  5
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   47  4
  18P LOSS WILD-TYPE 88  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     47    4
  18P LOSS WILD-TYPE   88    5
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               47                 88
  1                4                  5
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   13 58
  18P LOSS WILD-TYPE 14 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     13   58
  18P LOSS WILD-TYPE   14   99
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               13                 14
  MALE                 58                 99
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   54 10
  18P LOSS WILD-TYPE 70 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     54   10
  18P LOSS WILD-TYPE   70   32
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                54                 70
  YES               10                 32
[1] 2 2
[1] FALSE
D73V9, continuous
D73V10, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   44 27
  18P LOSS WILD-TYPE 44 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     44   27
  18P LOSS WILD-TYPE   44   69
                                   clus
vv                                  18P LOSS MUTATED 18P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   44                 44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               27                 69
[1] 2 2
[1] FALSE
D73V11, continuous
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   48  8  0  4
  18P LOSS WILD-TYPE 89  4  2  3
D73V12, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               48                 89
  R1                8                  4
  R2                0                  2
  RX                4                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED      13                         0    49
  18P LOSS WILD-TYPE    33                         5    65
D73V14, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                   13                 33
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                   49                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    3 30
  18P LOSS WILD-TYPE  3 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   30
  18P LOSS WILD-TYPE    3   58
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  3
  NOT HISPANIC OR LATINO               30                 58
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   59 43
  18Q LOSS WILD-TYPE 48 33
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               102                 81 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                43                 33 
$`18Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        31.27        14.30         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D 
        7.69         3.88        47.38        34.85        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       25.22         3.16        18.28         8.94        24.00        26.33 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU 
        4.70        32.61         3.32         7.17         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.43         2.60         3.75         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NS 
       35.97        12.92        13.48        16.47         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       27.12        83.24        52.57        10.36        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 
        7.99         7.59        38.40         6.35        53.95         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW 
        2.30        12.69         7.00        20.02         5.29         9.27 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L 
       46.19        18.21        19.73         0.85         2.63         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        23.41         9.96        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A93F TCGA-L5-A43H TCGA-L5-A88S TCGA-L5-A8NK TCGA-L7-A56G 
       68.02        24.03         0.30        15.48        13.55        10.85 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       13.25        12.59        22.39        12.85        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ 
        4.47        12.33        12.23        13.38        13.18        12.85 
TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        5.16         3.42        27.09        12.43        18.31         8.12 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       18.05         9.17        25.08        41.23         3.42         2.66 

$`18Q LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A7DP 
       58.55         7.63         5.92        13.94         4.21        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A939 TCGA-L5-A43E TCGA-L5-A4OI TCGA-L5-A4OJ 
      122.10        60.39        21.70        30.25        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88T 
       18.35         1.38         3.16        58.59         7.13        22.82 
TCGA-L5-A88Y TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW TCGA-R6-A6KZ 
        0.36        13.22         7.76         5.49        46.09         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-V5-A7RE TCGA-V5-AASX 
       16.31         7.04         9.30        15.78        16.44         8.98 
TCGA-VR-A8EQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
       22.82        15.68        33.27        35.21        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FE 
       18.64         9.30        17.03        12.82         4.67         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z 
       41.52         6.28         4.31        47.93        25.12         7.40 
TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       21.37         5.92        13.15        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.49        12.76        12.59        15.52        11.54 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        10.52        12.00        12.03        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ET 
       12.03        12.26        20.38        15.35        25.81         1.55 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I 
       28.11        33.70        18.18        52.27        11.24        15.91 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       14.37         2.10         1.32 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.30               0.13 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             83.24             122.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             12.85              13.22 
[1] "0.3 - 83.2 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         3        1        3        1        22        18
  18Q LOSS WILD-TYPE       5        4        3        0        25        13
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED          13          7          7          5        4
  18Q LOSS WILD-TYPE        12          7          2          2        1
                    vv
clus                 STAGE IVA
  18Q LOSS MUTATED           2
  18Q LOSS WILD-TYPE         2
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                22                 25
  STAGE IIB                18                 13
  STAGE III                13                 12
  STAGE IIIA                7                  7
  STAGE IIIB                7                  2
  STAGE IIIC                5                  2
  STAGE IV                  4                  1
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  18Q LOSS MUTATED      14 22 52  2
  18Q LOSS WILD-TYPE    18 21 35  3
D74V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               14                 18
  T2                  22                 21
  T3                  52                 35
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18Q LOSS MUTATED   37 38  9  5
  18Q LOSS WILD-TYPE 40 30  3  3
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               37                 40
  N1               38                 30
  N2                9                  3
  N3                5                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   72  6
  18Q LOSS WILD-TYPE 63  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     72    6
  18Q LOSS WILD-TYPE   63    3
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               72                 63
  1                6                  3
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   15 87
  18Q LOSS WILD-TYPE 12 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     15   87
  18Q LOSS WILD-TYPE   12   70
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               15                 12
  MALE                 87                 70
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   68 23
  18Q LOSS WILD-TYPE 56 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     68   23
  18Q LOSS WILD-TYPE   56   19
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                68                 56
  YES               23                 19
[1] 2 2
[1] FALSE
D74V9, continuous
D74V10, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   57 45
  18Q LOSS WILD-TYPE 31 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     57   45
  18Q LOSS WILD-TYPE   31   51
                                   clus
vv                                  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   57                 31
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               45                 51
[1] 2 2
[1] FALSE
D74V11, continuous
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED   71  9  1  4
  18Q LOSS WILD-TYPE 66  3  1  3
D74V12, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               71                 66
  R1                9                  3
  R2                1                  1
  RX                4                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED      24                         3    63
  18Q LOSS WILD-TYPE    22                         2    51
D74V14, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                   24                 22
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   63                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    4 46
  18Q LOSS WILD-TYPE  2 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4   46
  18Q LOSS WILD-TYPE    2   42
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               46                 42
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED   37 28
  19P LOSS WILD-TYPE 70 48
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                65                118 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                28                 48 
$`19P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30         7.63        16.24         4.21 
TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OP 
        3.88       122.10        47.38        30.25        26.33         7.17 
TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NJ 
       58.59         7.43         2.60         3.75         2.66        16.47 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-R6-A6DN 
       13.22         5.49         8.71        52.57        46.09         7.99 
TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-V5-AASW TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IG-A3YB 
        7.04        15.78         9.27        46.19        19.73         2.63 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FD 
        0.53        17.03        23.41         9.96        14.50        68.02 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A8NK TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
        4.31        47.93        13.55        10.85        10.45        12.66 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.38        15.35        13.25        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.76        12.85         4.47        12.33        12.23        13.18 
TCGA-LN-A8I0 TCGA-LN-A9FR TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ 
       13.38        12.26         3.42        25.81         8.12        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       52.27         9.17        25.08        14.37         2.66 

$`19P LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE 
       58.55         5.92        13.94         8.94        32.45         7.69 
TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       14.86        60.39        34.85        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       25.22         3.16        18.28         8.94        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       32.61        19.99        21.01        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88Y 
        3.16         4.90        29.00         7.13        22.82         0.36 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM 
        3.02        55.50        35.97        12.92        13.48         7.76 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.41        27.12        83.24        10.36        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        16.31        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30         2.89         2.30        12.69         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ TCGA-X8-AAAR TCGA-IC-A6RF 
        5.29        16.44         8.98        22.82        18.21        15.68 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21         0.85        20.78        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA 
        9.30         0.79        12.82         4.67        12.16        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A88S 
        3.68        41.52        24.03         6.28         0.30        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       25.12         7.40        21.37         5.92        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.33        13.15        12.59        12.62        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        11.54        12.33        13.22        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.00        12.03        13.18         0.13        12.03        12.85 
TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        5.16        20.38        15.35        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I 
       18.31        28.11        33.70        18.05        11.24        15.91 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       41.23         3.42         2.10         1.32 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.53               0.13 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            122.10              83.24 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            12.850             13.165 
[1] "0.5 - 122.1 (12.8)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1"  
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         2        2        1        1        15        14
  19P LOSS WILD-TYPE       6        3        5        0        32        17
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED          12          3          2          3        1
  19P LOSS WILD-TYPE        13         11          7          4        4
                    vv
clus                 STAGE IVA
  19P LOSS MUTATED           3
  19P LOSS WILD-TYPE         1
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  2                  3
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                15                 32
  STAGE IIB                14                 17
  STAGE III                12                 13
  STAGE IIIA                3                 11
  STAGE IIIB                2                  7
  STAGE IIIC                3                  4
  STAGE IV                  1                  4
  STAGE IVA                 3                  1
[1] 12  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                 T0+T1 T2 T3 T4
  19P LOSS MUTATED      10 14 36  0
  19P LOSS WILD-TYPE    22 29 51  5
D75V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               10                 22
  T2                  14                 29
  T3                  36                 51
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19P LOSS MUTATED   22 32  2  3
  19P LOSS WILD-TYPE 55 36 10  5
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               22                 55
  N1               32                 36
  N2                2                 10
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   50  4
  19P LOSS WILD-TYPE 85  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     50    4
  19P LOSS WILD-TYPE   85    5
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               50                 85
  1                4                  5
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    7 58
  19P LOSS WILD-TYPE 20 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7   58
  19P LOSS WILD-TYPE   20   99
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 58                 99
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   39 18
  19P LOSS WILD-TYPE 85 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     39   18
  19P LOSS WILD-TYPE   85   24
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                39                 85
  YES               18                 24
[1] 2 2
[1] FALSE
D75V9, continuous
D75V10, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   29 36
  19P LOSS WILD-TYPE 59 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     29   36
  19P LOSS WILD-TYPE   59   60
                                   clus
vv                                  19P LOSS MUTATED 19P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   29                 59
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               36                 60
[1] 2 2
[1] FALSE
D75V11, continuous
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED   47  3  1  2
  19P LOSS WILD-TYPE 90  9  1  5
D75V12, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               47                 90
  R1                3                  9
  R2                1                  1
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED      20                         4    33
  19P LOSS WILD-TYPE    26                         1    81
D75V14, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                   20                 26
  BLACK OR AFRICAN AMERICAN                4                  1
  WHITE                                   33                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V15, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2 30
  19P LOSS WILD-TYPE  4 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   30
  19P LOSS WILD-TYPE    4   58
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               30                 58
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED   32 20
  19Q LOSS WILD-TYPE 75 56
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                52                131 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                20                 56 
$`19Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-JY-A6F8 TCGA-JY-A6FH 
       25.78        31.27        14.30         4.21       122.10        47.38 
TCGA-L5-A43E TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A891 
       30.25         7.17        58.59         7.43         2.60         3.75 
TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NR TCGA-R6-A6DN TCGA-R6-A8W5 TCGA-R6-A8WC 
        2.66        13.22         8.71         7.99        15.78         2.30 
TCGA-ZR-A9CJ TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
       19.73         2.63         0.53        23.41         9.96        14.50 
TCGA-JY-A6FD TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L7-A56G TCGA-LN-A49L 
       68.02         4.31        47.93        15.48        10.85        10.45 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       12.66        13.38        13.15        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 
       12.49         4.47        12.33        12.23        13.18        13.38 
TCGA-LN-A9FR TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.26         3.42        25.81         8.12        18.18        52.27 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN 
        9.17        25.08        14.37         2.66 

$`19Q LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A938 
       32.45         7.69         3.88        14.86        60.39        34.85 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43I 
       21.70        23.18        31.56        25.22         3.16        18.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00        26.33         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       21.01        18.35         3.32         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE 
       29.00         7.13        22.82         0.36         3.02        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        12.92        13.48        16.47         7.76         5.49 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WG 
       38.40         6.35        53.95         9.30         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.02         5.29        16.44         9.27         8.98 
TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       22.82        46.19        18.21        15.68        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
        0.85        20.78        20.12        18.64         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE 
        0.79        12.82         4.67        12.16        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A88W TCGA-L5-A88Z 
       41.52        24.03         6.28         0.30        25.12         7.40 
TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       13.55        21.37         5.92        12.43        13.41        12.33 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       15.35        12.59        12.62        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 
       12.85        15.52        11.54        12.33        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       10.52        12.00        12.03        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER 
       12.85         5.16        20.38        15.35        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7B 
        1.55        18.31        28.11        33.70        18.05        11.24 
TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        41.23         3.42         2.10         1.32 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.53               0.13 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            122.10              83.24 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            12.625             13.220 
[1] "0.5 - 122.1 (12.6)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         2        2        1        0        13        11
  19Q LOSS WILD-TYPE       6        3        5        1        34        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           8          3          1          3        1
  19Q LOSS WILD-TYPE        17         11          8          4        4
                    vv
clus                 STAGE IVA
  19Q LOSS MUTATED           2
  19Q LOSS WILD-TYPE         2
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  2                  3
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                13                 34
  STAGE IIB                11                 20
  STAGE III                 8                 17
  STAGE IIIA                3                 11
  STAGE IIIB                1                  8
  STAGE IIIC                3                  4
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  19Q LOSS MUTATED       7 12 29  0
  19Q LOSS WILD-TYPE    25 31 58  5
D76V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1                7                 25
  T2                  12                 31
  T3                  29                 58
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19Q LOSS MUTATED   20 23  1  3
  19Q LOSS WILD-TYPE 57 45 11  5
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               20                 57
  N1               23                 45
  N2                1                 11
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   39  3
  19Q LOSS WILD-TYPE 96  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     39    3
  19Q LOSS WILD-TYPE   96    6
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               39                 96
  1                3                  6
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     6  46
  19Q LOSS WILD-TYPE  21 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6   46
  19Q LOSS WILD-TYPE   21  111
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                6                 21
  MALE                 46                111
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   29 15
  19Q LOSS WILD-TYPE 95 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     29   15
  19Q LOSS WILD-TYPE   95   27
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                29                 95
  YES               15                 27
[1] 2 2
[1] FALSE
D76V9, continuous
D76V10, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   19 33
  19Q LOSS WILD-TYPE 69 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     19   33
  19Q LOSS WILD-TYPE   69   63
                                   clus
vv                                  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   19                 69
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               33                 63
[1] 2 2
[1] FALSE
D76V11, continuous
                    vv
clus                 R0 R1 R2 RX
  19Q LOSS MUTATED   40  1  1  1
  19Q LOSS WILD-TYPE 97 11  1  6
D76V12, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               40                 97
  R1                1                 11
  R2                1                  1
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED      18                         4    24
  19Q LOSS WILD-TYPE    28                         1    90
D76V14, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                   18                 28
  BLACK OR AFRICAN AMERICAN                4                  1
  WHITE                                   24                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V15, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2 25
  19Q LOSS WILD-TYPE  4 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   25
  19Q LOSS WILD-TYPE    4   63
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               25                 63
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED   14  5
  20P LOSS WILD-TYPE 93 71
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                164 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 71 
$`20P LOSS MUTATED`
TCGA-2H-A9GI TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO 
       14.30        47.38         8.94        26.33        32.61         3.32 
TCGA-L5-A8NL TCGA-L5-A8NU TCGA-R6-A6XG TCGA-VR-A8EQ TCGA-JY-A6FA TCGA-JY-A6FD 
       13.22        83.24        38.40        22.82        44.75        68.02 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A7HW TCGA-LN-A7HY TCGA-S8-A6BW 
       12.66        13.41        12.46        12.00        12.03        20.38 
TCGA-XP-A8T8 
       14.37 

$`20P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        8.94        16.24         4.21        32.45         7.69         3.88 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       14.86       122.10        60.39        34.85        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OE 
       31.56        25.22         3.16        30.25        18.28        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        4.70        19.99        21.01        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       22.82         2.60         0.36         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM 
        2.66        35.97        12.92        13.48        16.47         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        27.12        52.57        46.09 
TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       10.36        33.11         7.82         7.99         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ 
       16.44         9.27         8.98        46.19        18.21        19.73 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       15.68        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ 
       47.93        15.48        25.12         7.40        13.55        21.37 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R 
       10.85         5.92        10.45        12.43        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       10.52        12.23        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-V5-AASV 
       12.03        12.85        12.26         5.16         3.42        15.35 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        15.91        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              3.32               0.13 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             83.24             122.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            14.370             12.835 
[1] "3.3 - 83.2 (14.4)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "2.6"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         1        0        1        0         6         4
  20P LOSS WILD-TYPE       7        5        5        1        41        27
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           4          0          0          1        0
  20P LOSS WILD-TYPE        21         14          9          6        5
                    vv
clus                 STAGE IVA
  20P LOSS MUTATED           0
  20P LOSS WILD-TYPE         4
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 6                 41
  STAGE IIB                 4                 27
  STAGE III                 4                 21
  STAGE IIIA                0                 14
  STAGE IIIB                0                  9
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  20P LOSS MUTATED       3  6  9  0
  20P LOSS WILD-TYPE    29 37 78  5
D77V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                3                 29
  T2                   6                 37
  T3                   9                 78
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20P LOSS MUTATED    8  8  1  1
  20P LOSS WILD-TYPE 69 60 11  7
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                8                 69
  N1                8                 60
  N2                1                 11
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    15   0
  20P LOSS WILD-TYPE 120   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     15    0
  20P LOSS WILD-TYPE  120    9
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               15                120
  1                0                  9
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  17
  20P LOSS WILD-TYPE  25 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   17
  20P LOSS WILD-TYPE   25  140
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 25
  MALE                 17                140
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12   4
  20P LOSS WILD-TYPE 112  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12    4
  20P LOSS WILD-TYPE  112   38
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                12                112
  YES                4                 38
[1] 2 2
[1] FALSE
D77V9, continuous
D77V10, binary
                    cls
clus                  0  1
  20P LOSS MUTATED   10  9
  20P LOSS WILD-TYPE 78 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     10    9
  20P LOSS WILD-TYPE   78   87
                                   clus
vv                                  20P LOSS MUTATED 20P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   10                 78
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                9                 87
[1] 2 2
[1] FALSE
D77V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    16   0   0   1
  20P LOSS WILD-TYPE 121  12   2   6
D77V12, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               16                121
  R1                0                 12
  R2                0                  2
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       7                         1     9
  20P LOSS WILD-TYPE    39                         4   105
D77V14, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    7                 39
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    9                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  7
  20P LOSS WILD-TYPE  5 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    7
  20P LOSS WILD-TYPE    5   81
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO                7                 81
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     6   2
  20Q LOSS WILD-TYPE 101  74
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                175 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 74 
$`20Q LOSS MUTATED`
TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OO TCGA-VR-A8EQ TCGA-JY-A6FA TCGA-LN-A7HW 
       47.38         8.94         3.32        22.82        44.75        12.00 
TCGA-LN-A9FR TCGA-S8-A6BW 
       12.26        20.38 

$`20Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A939 
        3.88        14.86       122.10        60.39        34.85        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43I 
       23.18        31.56        25.22         3.16        30.25        18.28 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00        26.33         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y 
       29.00         7.13         7.43        22.82         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.75         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       13.48        16.47        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         7.99         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ 
       16.44         9.27         8.98        46.19        18.21        19.73 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       15.68        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H 
       68.02         3.68        41.52        24.03         6.28         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK 
        4.31        47.93        15.48        25.12         7.40        13.55 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
       12.85         5.16         3.42        15.35        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              3.32               0.13 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             47.38             122.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             16.32              13.15 
[1] "3.3 - 47.4 (16.3)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "2"  
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0        0        1        0         1         3
  20Q LOSS WILD-TYPE       8        5        5        1        46        28
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           1          0          0          1        0
  20Q LOSS WILD-TYPE        24         14          9          6        5
                    vv
clus                 STAGE IVA
  20Q LOSS MUTATED           0
  20Q LOSS WILD-TYPE         4
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 1                 46
  STAGE IIB                 3                 28
  STAGE III                 1                 24
  STAGE IIIA                0                 14
  STAGE IIIB                0                  9
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  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                 T0+T1 T2 T3 T4
  20Q LOSS MUTATED       0  5  3  0
  20Q LOSS WILD-TYPE    32 38 84  5
D78V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                0                 32
  T2                   5                 38
  T3                   3                 84
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20Q LOSS MUTATED    2  4  1  1
  20Q LOSS WILD-TYPE 75 64 11  7
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                2                 75
  N1                4                 64
  N2                1                 11
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   0
  20Q LOSS WILD-TYPE 129   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  129    9
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                6                129
  1                0                  9
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   7
  20Q LOSS WILD-TYPE  26 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    7
  20Q LOSS WILD-TYPE   26  150
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 26
  MALE                  7                150
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   2
  20Q LOSS WILD-TYPE 119  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    2
  20Q LOSS WILD-TYPE  119   40
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 5                119
  YES                2                 40
[1] 2 2
[1] FALSE
D78V9, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 66 
        TCGA-IG-A7DP         TCGA-V5-A7RB         TCGA-V5-A7RE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-AA4D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-KH-A6WC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49K         TCGA-LN-A49L         TCGA-LN-A49M 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HY         TCGA-LN-A7HZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-AASV         TCGA-VR-A8EO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8ET 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7B         TCGA-VR-AA7D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D78V10, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    4  4
  20Q LOSS WILD-TYPE 84 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    4
  20Q LOSS WILD-TYPE   84   92
                                   clus
vv                                  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                    4                 84
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                4                 92
[1] 2 2
[1] FALSE
D78V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     7   0   0   1
  20Q LOSS WILD-TYPE 130  12   2   6
D78V12, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                7                130
  R1                0                 12
  R2                0                  2
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       3                         0     4
  20Q LOSS WILD-TYPE    43                         5   110
D78V14, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    3                 43
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  3
  20Q LOSS WILD-TYPE  6 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    3
  20Q LOSS WILD-TYPE    6   85
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO                3                 85
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   60 45
  21Q LOSS WILD-TYPE 47 31
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               105                 78 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                45                 31 
$`21Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR 
       25.78         7.63         5.92        13.94         8.94        32.45 
TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E 
        3.88       122.10        23.18        31.56         3.16        30.25 
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
       18.28         8.94        24.00         4.70        32.61        21.01 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        7.43         2.60         0.36         3.75         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       12.92        16.47        13.22         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       52.57        46.09        10.36        33.11         7.82         7.99 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06         7.04        38.40         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        2.89         2.30        12.69        16.44         9.27         8.98 
TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-ZR-A9CJ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       22.82        46.19        19.73        33.27         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A93F 
       20.12        18.64         0.53         0.79         9.96        24.03 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A8NK 
        0.30         4.31        47.93        15.48         7.40        13.55 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.85         5.92        12.43        13.41        13.38        13.15 
TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       13.25        12.76        12.85        12.33        13.22        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FQ 
       12.00        12.23        12.03        13.18        13.38        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       12.26         5.16        25.81        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 
       28.11        18.18        52.27        11.24         9.17        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN 
       14.37         2.10         2.66 

$`21Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        14.30        58.55        16.24         4.21         7.69 
TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E 
       14.86        60.39        47.38        34.85        21.70        25.22 
TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88T 
       26.33        19.99        18.35         3.32         1.38        22.82 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NU 
       55.50        35.97        13.48         7.76         5.49        83.24 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       16.31        53.95        15.78         7.00        20.02         5.29 
TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
       18.21        15.68        35.21         2.63         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       23.41        12.82         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A88W TCGA-L5-A8NQ 
       68.02         3.68        41.52         6.28        25.12        21.37 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       10.45        12.66        12.33        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.46        12.59        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A8I1 TCGA-LN-A9FO 
       11.54         4.47        25.25        10.52        13.18         0.13 
TCGA-LN-A9FP TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU 
       12.03        20.38         3.42        15.35        27.09        18.31 
TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       33.70        18.05        15.91        25.08         3.42         1.32 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.30               0.13 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            122.10              83.24 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            12.430             15.435 
[1] "0.3 - 122.1 (12.4)" "0.1 - 83.2 (15.4)" 
[1] "hr=" "1.4"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         6        3        5        1        21        14
  21Q LOSS WILD-TYPE       2        2        1        0        26        17
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED          16          7          6          5        3
  21Q LOSS WILD-TYPE         9          7          3          2        2
                    vv
clus                 STAGE IVA
  21Q LOSS MUTATED           2
  21Q LOSS WILD-TYPE         2
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   6                  2
  STAGE IA                  3                  2
  STAGE IB                  5                  1
  STAGE II                  1                  0
  STAGE IIA                21                 26
  STAGE IIB                14                 17
  STAGE III                16                  9
  STAGE IIIA                7                  7
  STAGE IIIB                6                  3
  STAGE IIIC                5                  2
  STAGE IV                  3                  2
  STAGE IVA                 2                  2
[1] 12  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                 T0+T1 T2 T3 T4
  21Q LOSS MUTATED      18 20 51  3
  21Q LOSS WILD-TYPE    14 23 36  2
D79V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               18                 14
  T2                  20                 23
  T3                  51                 36
  T4                   3                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  21Q LOSS MUTATED   42 37  7  6
  21Q LOSS WILD-TYPE 35 31  5  2
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               42                 35
  N1               37                 31
  N2                7                  5
  N3                6                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   75  5
  21Q LOSS WILD-TYPE 60  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     75    5
  21Q LOSS WILD-TYPE   60    4
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               75                 60
  1                5                  4
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   17 89
  21Q LOSS WILD-TYPE 10 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     17   89
  21Q LOSS WILD-TYPE   10   68
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               17                 10
  MALE                 89                 68
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   71 23
  21Q LOSS WILD-TYPE 53 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     71   23
  21Q LOSS WILD-TYPE   53   19
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                71                 53
  YES               23                 19
[1] 2 2
[1] FALSE
D79V9, continuous
D79V10, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   57 49
  21Q LOSS WILD-TYPE 31 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     57   49
  21Q LOSS WILD-TYPE   31   47
                                   clus
vv                                  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   57                 31
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               49                 47
[1] 2 2
[1] FALSE
D79V11, continuous
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   74 10  0  6
  21Q LOSS WILD-TYPE 63  2  2  1
D79V12, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               74                 63
  R1               10                  2
  R2                0                  2
  RX                6                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED      22                         2    69
  21Q LOSS WILD-TYPE    24                         3    45
D79V14, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                   22                 24
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                   69                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    4 45
  21Q LOSS WILD-TYPE  2 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   45
  21Q LOSS WILD-TYPE    2   43
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               45                 43
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   37 35
  22Q LOSS WILD-TYPE 70 41
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                72                111 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                35                 41 
$`22Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A4QS TCGA-JY-A6F8 
        8.94        16.24         4.21        32.45         3.88       122.10 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43I TCGA-L5-A4OE 
       47.38        34.85        31.56         3.16        18.28        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        4.70        32.61        58.59         4.90        29.00         7.13 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ 
       16.47        13.22         5.49         8.71        46.09        10.36 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.99         7.59         5.06        38.40        15.78         2.89 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EQ TCGA-ZR-A9CJ 
        7.00         5.29        16.44         9.27        22.82        19.73 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 
        2.63        18.64         0.53         0.79        23.41         4.67 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R 
        7.40        13.55         5.92        10.45        13.41        13.38 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HV TCGA-LN-A7HY 
       15.35        13.25        12.62        12.76        10.52        12.03 
TCGA-LN-A7HZ TCGA-VR-A8EO TCGA-VR-A8EU TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN 
       13.18        25.81        18.31        14.37         2.10         2.66 

$`22Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93C 
       25.78         7.69        14.86        60.39        21.70        23.18 
TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ 
       25.22        30.25         8.94        26.33        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OX 
       18.35         3.32         7.17         1.38         3.16         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NM TCGA-L5-A8NS 
       22.82         2.60         3.75        35.97         7.76        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
       27.12        83.24        52.57        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.04         6.35        53.95         9.30         2.30        12.69 
TCGA-S8-A6BV TCGA-V5-AASX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-IC-A6RF TCGA-IG-A3I8 
       20.02         8.98        46.19        18.21        15.68        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D 
       35.21         0.85        20.78        20.12         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       12.82         9.96        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49M 
       47.93        15.48        25.12        21.37        10.85        12.66 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 
       12.43        12.33        13.15        12.59        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.23        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP 
       12.26         5.16        20.38         3.42        15.35        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       52.27        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       41.23         3.42         1.32 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.36               0.13 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            122.10              83.24 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             13.05              13.15 
[1] "0.4 - 122.1 (13.1)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.4"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         5        0        3        0        13        11
  22Q LOSS WILD-TYPE       3        5        3        1        34        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED          15          4          3          3        3
  22Q LOSS WILD-TYPE        10         10          6          4        2
                    vv
clus                 STAGE IVA
  22Q LOSS MUTATED           3
  22Q LOSS WILD-TYPE         1
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   5                  3
  STAGE IA                  0                  5
  STAGE IB                  3                  3
  STAGE II                  0                  1
  STAGE IIA                13                 34
  STAGE IIB                11                 20
  STAGE III                15                 10
  STAGE IIIA                4                 10
  STAGE IIIB                3                  6
  STAGE IIIC                3                  4
  STAGE IV                  3                  2
  STAGE IVA                 3                  1
[1] 12  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                 T0+T1 T2 T3 T4
  22Q LOSS MUTATED      16 10 39  0
  22Q LOSS WILD-TYPE    16 33 48  5
D80V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1               16                 16
  T2                  10                 33
  T3                  39                 48
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  22Q LOSS MUTATED   24 35  3  3
  22Q LOSS WILD-TYPE 53 33  9  5
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               24                 53
  N1               35                 33
  N2                3                  9
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   53  6
  22Q LOSS WILD-TYPE 82  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     53    6
  22Q LOSS WILD-TYPE   82    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               53                 82
  1                6                  3
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   10 62
  22Q LOSS WILD-TYPE 17 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   62
  22Q LOSS WILD-TYPE   17   95
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               10                 17
  MALE                 62                 95
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   45 19
  22Q LOSS WILD-TYPE 79 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     45   19
  22Q LOSS WILD-TYPE   79   23
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                45                 79
  YES               19                 23
[1] 2 2
[1] FALSE
D80V9, continuous
D80V10, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   48 24
  22Q LOSS WILD-TYPE 40 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     48   24
  22Q LOSS WILD-TYPE   40   72
                                   clus
vv                                  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                   48                 40
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               24                 72
[1] 2 2
[1] FALSE
D80V11, continuous
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   55  6  0  2
  22Q LOSS WILD-TYPE 82  6  2  5
D80V12, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               55                 82
  R1                6                  6
  R2                0                  2
  RX                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED      13                         1    45
  22Q LOSS WILD-TYPE    33                         4    69
D80V14, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                   13                 33
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   45                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V15, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    2 30
  22Q LOSS WILD-TYPE  4 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   30
  22Q LOSS WILD-TYPE    4   58
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               30                 58
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED   37 23
  XP LOSS WILD-TYPE 70 53
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               60               123 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               23                53 
$`XP LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A4QS TCGA-JY-A6FH 
       25.78        14.30         4.21        32.45         3.88        47.38 
TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OJ 
       34.85        23.18        30.25        18.28        24.00        21.01 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR 
       18.35         7.17         3.75        13.48        16.47         8.71 
TCGA-L5-A8NS TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A8WC 
       13.41        46.09        33.11         7.99         5.06         2.30 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-IG-A3QL 
       12.69        20.02        16.44         9.27         8.98        35.21 
TCGA-IG-A3YA TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
       20.78         0.53        23.41        12.82         9.96         4.67 
TCGA-JY-A6FA TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y 
       44.75         5.92        12.66        12.33        13.38        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.59        22.39        11.54        13.22        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FR TCGA-VR-A8EO TCGA-VR-A8EU 
       12.00        13.38         0.13        12.26        25.81        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        8.12        52.27        15.91        14.37         3.42         2.10 

$`XP LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A939 
       16.24         7.69        14.86       122.10        60.39        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
       31.56        25.22         3.16         8.94        26.33         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       32.61        19.99         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        22.82         2.60 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         7.76         5.49        27.12        83.24        52.57 
TCGA-L7-A6VZ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       10.36         7.82         7.59        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO 
        6.35        53.95         9.30        15.78         2.89         7.00 
TCGA-V5-A7RB TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF 
        5.29        22.82        46.19        18.21        19.73        15.68 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       33.27         0.85         2.63        20.12        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE 
       17.03         0.79        14.50        12.16        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM 
       41.52        24.03         6.28         0.30         4.31        47.93 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G 
       15.48        25.12         7.40        13.55        21.37        10.85 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45        12.43        13.41        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       13.25        12.62        12.49        12.76        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY 
       15.52        12.33         4.47        12.33        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FU TCGA-S8-A6BW 
       13.18        13.18        12.03        12.85         5.16        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX 
        3.42        15.35        27.09        12.43         1.55        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 
       33.70        18.18        18.05        11.24         9.17        25.08 
TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23         1.32         2.66 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.13              0.30 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            52.27            122.10 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            13.38             12.85 
[1] "0.1 - 52.3 (13.4)"  "0.3 - 122.1 (12.8)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         2        1        2        0        17        10
  XP LOSS WILD-TYPE       6        4        4        1        30        21
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           8          6          6          0        1
  XP LOSS WILD-TYPE        17          8          3          7        4
                   vv
clus                STAGE IVA
  XP LOSS MUTATED           0
  XP LOSS WILD-TYPE         4
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 1                 4
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA               17                30
  STAGE IIB               10                21
  STAGE III                8                17
  STAGE IIIA               6                 8
  STAGE IIIB               6                 3
  STAGE IIIC               0                 7
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  XP LOSS MUTATED       7 15 30  2
  XP LOSS WILD-TYPE    25 28 57  3
D81V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1               7                25
  T2                 15                28
  T3                 30                57
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  XP LOSS MUTATED   27 21  6  0
  XP LOSS WILD-TYPE 50 47  6  8
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              27                50
  N1              21                47
  N2               6                 6
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   48  1
  XP LOSS WILD-TYPE 87  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     48    1
  XP LOSS WILD-TYPE   87    8
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              48                87
  1               1                 8
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     4  56
  XP LOSS WILD-TYPE  23 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      4   56
  XP LOSS WILD-TYPE   23  101
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               4                23
  MALE                56               101
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   39 12
  XP LOSS WILD-TYPE 85 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     39   12
  XP LOSS WILD-TYPE   85   30
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               39                85
  YES              12                30
[1] 2 2
[1] FALSE
D81V9, continuous
D81V10, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   29 31
  XP LOSS WILD-TYPE 59 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     29   31
  XP LOSS WILD-TYPE   59   65
                                   clus
vv                                  XP LOSS MUTATED XP LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  29                59
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              31                65
[1] 2 2
[1] FALSE
D81V11, continuous
                   vv
clus                R0 R1 R2 RX
  XP LOSS MUTATED   46  3  1  2
  XP LOSS WILD-TYPE 91  9  1  5
D81V12, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              46                91
  R1               3                 9
  R2               1                 1
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED      21                         1    32
  XP LOSS WILD-TYPE    25                         4    82
D81V14, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                  21                25
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  32                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V15, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    2 32
  XP LOSS WILD-TYPE  4 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   32
  XP LOSS WILD-TYPE    4   56
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              32                56
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   24 16
  XQ LOSS WILD-TYPE 83 60
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               40               143 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16                60 
$`XQ LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-JY-A6FH TCGA-JY-A938 TCGA-L5-A43E 
       25.78         4.21        32.45        47.38        34.85        30.25 
TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
       18.28        24.00        21.01        18.35         7.17         3.16 
TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NW TCGA-M9-A5M8 
        3.75        13.48        16.47         8.71        46.09        33.11 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASW 
        7.99         5.06         2.30        12.69        16.44         9.27 
TCGA-V5-AASX TCGA-IG-A625 TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A5 
        8.98        12.82        12.33        13.38        12.46        22.39 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-V5-A7RC 
       11.54        13.22        25.25        10.52        12.00         3.42 
TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       25.81        52.27         3.42         2.10 

$`XQ LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 
        8.94        16.24         7.69         3.88        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
       60.39        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO 
        8.94        26.33         4.70        32.61        19.99         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       22.82         2.60         0.36         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NS 
       35.97        12.92        13.22         7.76         5.49        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-Q9-A6FW TCGA-R6-A6DQ 
       27.12        83.24        52.57        10.36         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-VR-A8EQ 
       15.78         2.89         7.00        20.02         5.29        22.82 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       46.19        18.21        19.73        15.68        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.53        17.03         0.79        23.41         9.96         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S 
       24.03         6.28         0.30         4.31        47.93        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K 
       25.12         7.40        13.55        21.37        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.59        12.85        15.52        12.33         4.47        12.33 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-AASV 
       12.03        12.85        12.26         5.16        20.38        15.35 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        18.18        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         1.32         2.66 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2.10              0.13 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            52.27            122.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.02             13.15 
[1] "2.1 - 52.3 (13.0)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1"  
D82V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         2        2        2        0        11         4
  XQ LOSS WILD-TYPE       6        3        4        1        36        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           6          3          2          0        0
  XQ LOSS WILD-TYPE        19         11          7          7        5
                   vv
clus                STAGE IVA
  XQ LOSS MUTATED           0
  XQ LOSS WILD-TYPE         4
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA               11                36
  STAGE IIB                4                27
  STAGE III                6                19
  STAGE IIIA               3                11
  STAGE IIIB               2                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  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                T0+T1 T2 T3 T4
  XQ LOSS MUTATED       6  8 19  0
  XQ LOSS WILD-TYPE    26 35 68  5
D82V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1               6                26
  T2                  8                35
  T3                 19                68
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  XQ LOSS MUTATED   18 13  2  0
  XQ LOSS WILD-TYPE 59 55 10  8
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              18                59
  N1              13                55
  N2               2                10
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    28   0
  XQ LOSS WILD-TYPE 107   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     28    0
  XQ LOSS WILD-TYPE  107    9
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              28               107
  1               0                 9
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3  37
  XQ LOSS WILD-TYPE  24 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   37
  XQ LOSS WILD-TYPE   24  120
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                24
  MALE                37               120
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   25  8
  XQ LOSS WILD-TYPE 99 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     25    8
  XQ LOSS WILD-TYPE   99   34
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               25                99
  YES               8                34
[1] 2 2
[1] FALSE
D82V9, continuous
D82V10, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   25 15
  XQ LOSS WILD-TYPE 63 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     25   15
  XQ LOSS WILD-TYPE   63   81
                                   clus
vv                                  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA  NOS                  25                63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              15                81
[1] 2 2
[1] FALSE
D82V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    28   3   0   2
  XQ LOSS WILD-TYPE 109   9   2   5
D82V12, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              28               109
  R1               3                 9
  R2               0                 2
  RX               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED      10                         1    24
  XQ LOSS WILD-TYPE    36                         4    90
D82V14, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                  10                36
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  24                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V15, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1 19
  XQ LOSS WILD-TYPE  5 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   19
  XQ LOSS WILD-TYPE    5   69
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              19                69
[1] 2 2
[1] FALSE
