[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/22506419/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/22519067/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 
               38               146 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               38               146 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               64               120 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               64               120 
[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 
               47               137 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               47               137 
[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 
               17               167 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               17               167 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               167 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               167 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               75               109 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               75               109 
[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 
               39               145 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               39               145 
[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 
              109                75 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              109                75 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               87                97 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               87                97 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               67               117 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               67               117 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              102                82 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              102                82 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               167 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               167 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               34               150 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               34               150 
[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 
                31                153 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                31                153 
[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 
                57                127 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                57                127 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                37                147 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                37                147 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                44                140 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                44                140 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                49                135 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                49                135 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                31                153 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                31                153 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                40                144 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                40                144 
[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 
                32                152 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                152 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                44                140 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                44                140 
[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 
                24                160 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                24                160 
[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 
                40                144 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                40                144 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               107                 77 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               107                 77 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               114                 70 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               114                 70 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                16                168 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                16                168 
[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 
               25               159 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               25               159 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               41               143 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               41               143 
[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 
               10               174 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               174 
[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 
               92                92 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               92                92 
[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 
               88                96 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               88                96 
[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 
               87                97 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               87                97 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               146 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               146 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               40               144 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               40               144 
[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 
               23               161 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               23               161 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               62               122 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               62               122 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               163 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               163 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              100                84 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              100                84 
[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 
                51                133 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                51                133 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                50                134 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                50                134 
[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 
                60                124 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                124 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                34                150 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                34                150 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                32                152 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                32                152 
[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 
                56                128 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                56                128 
[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 
                72                112 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                72                112 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                26                158 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                26                158 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                69                115 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                69                115 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               103                 81 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               103                 81 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                64                120 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                64                120 
[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 
                 6                178 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                178 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               108                 76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               108                 76 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                73                111 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                73                111 
[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 
               39               145 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39               145 
[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=96,	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 18
  1P GAIN WILD-TYPE 88 58
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               38               146 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               18                58 
$`1P GAIN MUTATED`
TCGA-L5-A88Y TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A8O2 
        0.36        13.94        35.21        17.03        23.41         4.67 
TCGA-JY-A93E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A893 
       25.22        47.93        18.35         7.43         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ 
        2.66        13.22        13.41        52.57        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49X TCGA-LN-A4MR TCGA-LN-A8I0 TCGA-LN-A9FO 
        5.92        10.45        12.62        13.22        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8W5 
       12.03        12.85        12.26        16.31        38.40        15.78 
TCGA-R6-A8WG TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-X8-AAAR TCGA-XP-A8T6 
       12.69         3.42        22.82         8.12        18.21        25.08 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

$`1P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        5.16        20.02        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63         5.92         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 
       18.64         3.88         9.30         0.53         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       26.33        32.61        21.01         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
        2.60        25.12         7.40        55.50        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       83.24        46.09        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-A49Y 
       13.38        13.15        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-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I1 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       13.18        33.11         7.82         8.02         7.59         5.06 
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-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        12.43         1.55        18.31 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        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 
            52.57            122.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           13.035            13.035 
[1] "0.1 - 52.6 (13.0)"  "0.3 - 122.1 (13.0)"
[1] "hr=" "1.4"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         1        1        0        0        10         8
  1P GAIN WILD-TYPE       7        4        6        1        37        23
                   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               10                37
  STAGE IIB                8                23
  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  9 16  0
  1P GAIN WILD-TYPE    24 34 71  5
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1               8                24
  T2                  9                34
  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
  1P GAIN MUTATED   16 13  2  2
  1P GAIN WILD-TYPE 61 55 10  6
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              16                61
  N1              13                55
  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    25   2
  1P GAIN WILD-TYPE 110   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     25    2
  1P GAIN WILD-TYPE  110    7
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              25               110
  1               2                 7
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     4  34
  1P GAIN WILD-TYPE  23 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4   34
  1P GAIN WILD-TYPE   23  123
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               4                23
  MALE                34               123
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   24  9
  1P GAIN WILD-TYPE 99 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     24    9
  1P GAIN WILD-TYPE   99   34
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               24                99
  YES               9                34
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   19 19
  1P GAIN WILD-TYPE 69 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     19   19
  1P GAIN WILD-TYPE   69   77
                                   clus
vv                                  1P GAIN MUTATED 1P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  19                69
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              19                77
[1] 2 2
[1] FALSE
D1V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    28   0   0   2
  1P GAIN WILD-TYPE 109  12   2   5
D1V12, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              28               109
  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    23
  1P GAIN WILD-TYPE    35                         2    91
D1V14, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                  11                35
  BLACK OR AFRICAN AMERICAN               3                 2
  WHITE                                  23                91
[1] 3 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 31
  1Q GAIN WILD-TYPE 75 45
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               64               120 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               31                45 
$`1Q GAIN MUTATED`
TCGA-L5-A88Y TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC 
        0.36        13.94         8.94        35.21         0.85        20.12 
TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 
       18.64        17.03         0.79        23.41        12.82         4.67 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
       31.56        25.22         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       18.35         7.43         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NV 
        2.66        12.92        13.22         5.49        13.41        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V 
       10.85        10.36         5.92        10.45        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.62        12.49        12.76        13.22         4.47        12.33 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.00        13.18        13.38         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RC 
       12.26        16.31        38.40        15.78        12.69         3.42 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA4D TCGA-VR-AA7I TCGA-X8-AAAR 
       22.82         8.12        28.11        46.19        15.91        18.21 
TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       25.08         2.10         1.32        19.73 

$`1Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        5.16        20.02        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        7.63         5.92        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       33.27        20.78         2.63         3.88         9.30         0.53 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OO 
       24.03         6.28         3.16        30.25        21.01         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-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.13        15.48         2.60        25.12        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW 
       13.55         7.76        21.37         8.71        83.24        46.09 
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-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       13.25        12.46        12.59        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       15.52        11.54        12.33        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.33        13.18        33.11         7.82         8.02 
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-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         2.30         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         8.98        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 
           12.835            13.215 
[1] "0.1 - 55.5 (12.8)"  "0.5 - 122.1 (13.2)"
[1] "hr=" "1.5"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         2        1        1        0        16        13
  1Q GAIN WILD-TYPE       6        4        5        1        31        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               16                31
  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 28  2
  1Q GAIN WILD-TYPE    18 28 59  3
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              14                18
  T2                 15                28
  T3                 28                59
  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   26 27  3  3
  1Q GAIN WILD-TYPE 51 41  9  5
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              26                51
  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   47  5
  1Q GAIN WILD-TYPE 88  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     47    5
  1Q GAIN WILD-TYPE   88    4
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              47                88
  1               5                 4
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    5 59
  1Q GAIN WILD-TYPE 22 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   59
  1Q GAIN WILD-TYPE   22   98
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               5                22
  MALE                59                98
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   40 17
  1Q GAIN WILD-TYPE 83 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     40   17
  1Q GAIN WILD-TYPE   83   26
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               40                83
  YES              17                26
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   27 37
  1Q GAIN WILD-TYPE 61 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     27   37
  1Q GAIN WILD-TYPE   61   59
                                   clus
vv                                  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  27                61
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              37                59
[1] 2 2
[1] FALSE
D2V11, continuous
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   49  1  2  2
  1Q GAIN WILD-TYPE 88 11  0  5
D2V12, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              49                88
  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    38
  1Q GAIN WILD-TYPE    26                         2    76
D2V14, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                  20                26
  BLACK OR AFRICAN AMERICAN               3                 2
  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"
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   33 28
  2P GAIN WILD-TYPE 75 48
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               61               123 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               28                48 
$`2P GAIN MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A88Y TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A4P3 
       15.68         4.31         0.36        13.94         8.94        18.64 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH 
       23.41         4.67        44.75        25.22        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88V 
       47.93        18.35         3.32         3.16         7.13         2.60 
TCGA-L5-A8NE TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       55.50        52.57        10.85        10.36         5.92        10.45 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.38        13.15        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.59        12.85        12.33        12.33        25.25        12.00 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.33        13.18        12.85        12.26         8.02         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-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU 
       12.69        20.38         3.42        15.35        27.09        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR 
        8.12        28.11        33.70        46.19        11.24        18.21 
TCGA-XP-A8T6 
       25.08 

$`2P GAIN WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82        35.97        27.12         5.16        20.02 
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-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16       122.10        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ 
        3.16        30.25         0.30        21.01         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W 
       58.59         4.90        29.00         7.43        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N 
        8.71        13.41        83.24        46.09        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-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       33.11         7.82         9.30        15.78         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        7.00         5.29        16.44         9.27         8.98        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       22.82        12.43         1.55        18.18        52.27        18.05 
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 TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.36              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             55.5             122.1 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            12.76             13.22 
[1] "0.4 - 55.5 (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        1        1        13        14
  2P GAIN WILD-TYPE       7        2        5        0        34        17
                   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                 1                 5
  STAGE II                 1                 0
  STAGE IIA               13                34
  STAGE IIB               14                17
  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      12 14 24  0
  2P GAIN WILD-TYPE    20 29 63  5
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              12                20
  T2                 14                29
  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   23 21  3  3
  2P GAIN WILD-TYPE 54 47  9  5
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              23                54
  N1              21                47
  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 86 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     37   17
  2P GAIN WILD-TYPE   86   26
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               37                86
  YES              17                26
[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 36
  2P GAIN WILD-TYPE  4 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   36
  2P GAIN WILD-TYPE    4   52
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              36                52
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   26 21
  2Q GAIN WILD-TYPE 82 55
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               47               137 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21                55 
$`2Q GAIN MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A88Y TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A5S3 
       15.68         4.31         0.36        13.94         8.94        23.41 
TCGA-JY-A6FA TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO 
       44.75        25.22        26.33        32.61        47.93         3.32 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K 
        7.13         2.60        55.50        52.57        10.85         5.92 
TCGA-LN-A49R TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A5U6 
       13.38        12.59        12.49        12.59        12.85        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR 
       25.25        12.00        12.33        13.18        12.85        12.26 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP 
        6.35        53.95        12.69         3.42        16.44        27.09 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T6 
       18.31        28.11        46.19        18.21        25.08 

$`2Q GAIN WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82        35.97        27.12         5.16        20.02 
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-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
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-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ 
       24.03         6.28         3.16        30.25         0.30        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-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
       29.00         7.43        15.48        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        46.09        10.36        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-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.62        12.46        12.76        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        13.22         4.47        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6L6 
       13.18        13.38         0.13        12.03        33.11         7.04 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.89         2.30         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        5.29        15.35         9.27         8.98        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43         1.55         8.12        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 TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  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 
            12.85             13.15 
[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        2        1        1         9        11
  2Q GAIN WILD-TYPE       7        3        5        0        38        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           4          1          2          1        1
  2Q GAIN WILD-TYPE        21         13          7          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                 2                 3
  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               2                 7
  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      11 11 15  0
  2Q GAIN WILD-TYPE    21 32 72  5
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              11                21
  T2                 11                32
  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
  2Q GAIN MUTATED   17 17  2  1
  2Q GAIN WILD-TYPE 60 51 10  7
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              17                60
  N1              17                51
  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"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    29   2
  2Q GAIN WILD-TYPE 106   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     29    2
  2Q GAIN WILD-TYPE  106    7
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              29               106
  1               2                 7
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     6  41
  2Q GAIN WILD-TYPE  21 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      6   41
  2Q GAIN WILD-TYPE   21  116
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               6                21
  MALE                41               116
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   30 12
  2Q GAIN WILD-TYPE 93 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     30   12
  2Q GAIN WILD-TYPE   93   31
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               30                93
  YES              12                31
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   23 24
  2Q GAIN WILD-TYPE 65 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     23   24
  2Q GAIN WILD-TYPE   65   72
                                   clus
vv                                  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  23                65
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              24                72
[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      14                         3    26
  2Q GAIN WILD-TYPE    32                         2    88
D4V14, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                  14                32
  BLACK OR AFRICAN AMERICAN               3                 2
  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"
D4V15, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2 27
  2Q GAIN WILD-TYPE  4 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   27
  2Q GAIN WILD-TYPE    4   61
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              27                61
[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 94 59
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               31               153 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17                59 
$`3P GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IC-A6RE 
        4.31        27.12         5.16        31.27        16.24         7.69 
TCGA-IG-A4P3 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4OR 
       18.64        23.18        25.22         0.30        47.93         3.16 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
        3.75        55.50        52.57        10.85        10.36        10.45 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A4A1 TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG 
       13.41        13.38        12.59         5.06        53.95        12.69 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EX TCGA-VR-AA7B TCGA-XP-A8T8 
        9.27        22.82        12.43        28.11        11.24        14.37 
TCGA-ZR-A9CJ 
       19.73 

$`3P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36        35.97        20.02 
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-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
        3.68        41.52        47.38        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       13.41        83.24        46.09         5.92        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.15        15.35        12.59        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35         8.98        25.81        27.09         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
        9.17        15.91        18.21        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        2.10         1.32         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 
            13.38             12.92 
[1] "0.3 - 55.5 (13.4)"  "0.1 - 122.1 (12.9)"
[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         4         7
  3P GAIN WILD-TYPE       8        3        6        1        43        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           4          1          2          2        1
  3P GAIN WILD-TYPE        21         13          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                4                43
  STAGE IIB                7                24
  STAGE III                4                21
  STAGE IIIA               1                13
  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    8 13  2  3
  3P GAIN WILD-TYPE 69 55 10  5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               8                69
  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"
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    18  11
  3P GAIN WILD-TYPE 105  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     18   11
  3P GAIN WILD-TYPE  105   32
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               18               105
  YES              11                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       5                         2    20
  3P GAIN WILD-TYPE    41                         3    94
D5V14, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   5                41
  BLACK OR AFRICAN AMERICAN               2                 3
  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"
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   46 31
  3Q GAIN WILD-TYPE 62 45
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               77               107 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               31                45 
$`3Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GH 
       60.39         4.31        35.97        27.12         5.16        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       58.55         7.63        16.24         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63        18.64         3.88         0.53        17.03 
TCGA-IG-A97H TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4OR 
       14.50        23.18        25.22         0.30        47.93         3.16 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.13        15.48         2.60         3.75        55.50         2.66 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G 
       16.47        13.22         8.71        13.41        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.36        10.45        12.43        13.41        13.38        13.15 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.59        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A8HZ TCGA-LN-A8I1 
       15.52        11.54        12.33        10.52        12.33        13.18 
TCGA-LN-A9FQ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG 
       12.85         8.02         7.59         5.06        53.95        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
       20.38         3.42         9.27        22.82        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 TCGA-ZR-A9CJ 
        9.17        41.23        14.37         1.32        19.73 

$`3Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GI 
       19.99        22.82         0.36        20.02        25.78        14.30 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YA 
        5.92        13.94         8.94         4.21        32.45        20.78 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
       20.12         9.30         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
        3.68        41.52        47.38        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH 
       29.00         7.43        25.12         7.40         3.02        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.48        13.55         7.76         5.49        21.37        83.24 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49W 
       46.09         5.92        12.66        12.33        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.62        12.46        12.85        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       25.25        12.00        12.23        12.03        13.18        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
        0.13        12.03        12.26        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        2.30         7.00         5.29        16.44        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7I 
       25.81        27.09         1.55        18.18        46.19        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       18.21        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 
            12.76             13.22 
[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   46 24
  3Q GAIN WILD-TYPE 77 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     46   24
  3Q GAIN WILD-TYPE   77   19
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               46                77
  YES              24                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  7
  4P GAIN WILD-TYPE 98 69
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               17               167 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7                69 
$`4P GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-L5-A4ON 
       18.28         4.31         2.63        23.41       122.10        18.35 
TCGA-L5-A8NE TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A5U5 TCGA-LN-A7HY TCGA-R6-A6XG 
       55.50        52.57        10.85         4.47        12.03        38.40 
TCGA-R6-A6Y0 TCGA-VR-A8EO TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-AAPN 
       53.95        25.81        18.21        25.08         2.66 

$`4P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        7.69        33.27        35.21         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
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-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        83.24        46.09        10.36         5.92 
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-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       46.19        18.05        11.24         9.17        15.91        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32        19.73 

  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 
            18.35             12.85 
[1] "2.6 - 122.1 (18.4)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.7"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         1        0        0        0         3         5
  4P GAIN WILD-TYPE       7        5        6        1        44        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                3                44
  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  2  9  0
  4P GAIN WILD-TYPE    29 41 78  5
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               3                29
  T2                  2                41
  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    6  8  0  0
  4P GAIN WILD-TYPE 71 60 12  8
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               6                71
  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     9   1
  4P GAIN WILD-TYPE 126   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      9    1
  4P GAIN WILD-TYPE  126    8
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               9               126
  1               1                 8
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  16
  4P GAIN WILD-TYPE  26 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   16
  4P GAIN WILD-TYPE   26  141
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                26
  MALE                16               141
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11   4
  4P GAIN WILD-TYPE 112  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    4
  4P GAIN WILD-TYPE  112   39
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               11               112
  YES               4                39
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    8  9
  4P GAIN WILD-TYPE 80 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8    9
  4P GAIN WILD-TYPE   80   87
                                   clus
vv                                  4P GAIN MUTATED 4P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   8                80
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               9                87
[1] 2 2
[1] FALSE
D7V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     9   1   1   1
  4P GAIN WILD-TYPE 128  11   1   6
D7V12, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               9               128
  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       2                         2    13
  4P GAIN WILD-TYPE    44                         3   101
D7V14, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   2                44
  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"
D7V15, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  9
  4P GAIN WILD-TYPE  5 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    9
  4P GAIN WILD-TYPE    5   79
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO               9                79
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   10  7
  4Q GAIN WILD-TYPE 98 69
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               167 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7                69 
$`4Q GAIN MUTATED`
TCGA-IG-A3YA TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A8NE 
       20.78        23.41       122.10         0.30        18.35        55.50 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HY TCGA-R6-A6Y0 
       52.57        10.85        15.52        11.54        12.03        53.95 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EW TCGA-X8-AAAR TCGA-Z6-AAPN 
        3.42        25.81         8.12        18.21         2.66 

$`4Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        20.02        25.78        31.27        14.30 
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-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         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-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37         8.71        13.41        83.24        46.09        10.36 
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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.85        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         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-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31        28.11        33.70        18.18        52.27        46.19 
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-ZR-A9CJ 
       14.37         3.42         2.10         1.32        19.73 

  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 
            18.21             12.85 
[1] "0.3 - 122.1 (18.2)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         1        0        0        0         5         3
  4Q GAIN WILD-TYPE       7        5        6        1        42        28
                   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                3                28
  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  3  7  1
  4Q GAIN WILD-TYPE    29 40 80  4
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               3                29
  T2                  3                40
  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  5  1  0
  4Q GAIN WILD-TYPE 69 63 11  8
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               8                69
  N1               5                63
  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    12   0
  4Q GAIN WILD-TYPE 123   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     12    0
  4Q GAIN WILD-TYPE  123    9
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              12               123
  1               0                 9
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  16
  4Q GAIN WILD-TYPE  26 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   16
  4Q GAIN WILD-TYPE   26  141
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                26
  MALE                16               141
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    13   3
  4Q GAIN WILD-TYPE 110  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     13    3
  4Q GAIN WILD-TYPE  110   40
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               13               110
  YES               3                40
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    6 11
  4Q GAIN WILD-TYPE 82 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6   11
  4Q GAIN WILD-TYPE   82   85
                                   clus
vv                                  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   6                82
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              11                85
[1] 2 2
[1] FALSE
D8V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    11   1   0   0
  4Q GAIN WILD-TYPE 126  11   2   7
D8V12, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              11               126
  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                         2    11
  4Q GAIN WILD-TYPE    42                         3   103
D8V14, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   4                42
  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"
D8V15, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0 10
  4Q GAIN WILD-TYPE  6 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   10
  4Q GAIN WILD-TYPE    6   78
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  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 61 48
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               75               109 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               28                48 
$`5P GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG 
       18.28         4.31         8.94        19.99         0.36        35.97 
TCGA-Q9-A6FU TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YB 
        5.16        14.30         5.92        32.45        33.27         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
       20.12        18.64         0.79        23.41        14.50        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H 
       68.02         3.68        47.38        31.56        25.22         0.30 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT 
       32.61        47.93         3.32         7.17         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK 
       29.00         7.13        15.48        55.50        12.92        13.55 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W 
       52.57        10.85        10.36        13.41        13.38        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.46        12.59        12.59        12.85        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
        4.47        12.33        12.00        12.23        13.18        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 
       13.18        12.85        12.26         5.06        16.31        53.95 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EY 
        7.00        20.38         3.42        27.09        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       52.27        18.05        15.91        25.08        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        2.10         1.32        19.73 

$`5P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T 
       15.68        60.39        34.85        24.00         4.70        22.82 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       27.12        20.02        25.78        31.27        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL 
       13.94         8.94        16.24         4.21         7.69        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.78         3.88         9.30         0.53        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       41.52        21.70        23.18        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
       30.25        26.33        21.01        18.35         1.38        58.59 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43         2.60        25.12         7.40         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-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K 
       21.37         8.71        13.41        83.24        46.09         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        12.62        12.49        12.76        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FO 
       11.54        25.25        10.52        12.03        13.38         0.13 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
       12.03        33.11         7.82         8.02         7.59         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-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       12.69         5.29        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 
       18.18        46.19        11.24         9.17        18.21        41.23 
TCGA-Z6-AAPN 
        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 
            13.22             12.69 
[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        3
  5P GAIN WILD-TYPE        15          6          7          2        2
                   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                 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
  5P GAIN MUTATED       9 18 42  1
  5P GAIN WILD-TYPE    23 25 45  4
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1               9                23
  T2                 18                25
  T3                 42                45
  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  5
  5P GAIN WILD-TYPE 46 39  8  3
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              31                46
  N1              29                39
  N2               4                 8
  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"
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   54  4
  5P GAIN WILD-TYPE 81  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     54    4
  5P GAIN WILD-TYPE   81    5
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              54                81
  1               4                 5
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   13 62
  5P GAIN WILD-TYPE 14 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     13   62
  5P GAIN WILD-TYPE   14   95
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              13                14
  MALE                62                95
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   51 17
  5P GAIN WILD-TYPE 72 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     51   17
  5P GAIN WILD-TYPE   72   26
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               51                72
  YES              17                26
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   27 48
  5P GAIN WILD-TYPE 61 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     27   48
  5P GAIN WILD-TYPE   61   48
                                   clus
vv                                  5P GAIN MUTATED 5P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  27                61
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              48                48
[1] 2 2
[1] FALSE
D9V11, continuous
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   54  7  2  4
  5P GAIN WILD-TYPE 83  5  0  3
D9V12, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              54                83
  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    44
  5P GAIN WILD-TYPE    25                         1    70
D9V14, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                  21                25
  BLACK OR AFRICAN AMERICAN               4                 1
  WHITE                                  44                70
[1] 3 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  6
  5Q GAIN WILD-TYPE 94 70
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               164 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                70 
$`5Q GAIN MUTATED`
TCGA-L5-A43M TCGA-L5-A4OI TCGA-IG-A3I8 TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH 
        8.94        19.99        33.27        25.22         0.30        32.61 
TCGA-L5-A4OO TCGA-L5-A88S TCGA-L7-A6VZ TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
        3.32        15.48        10.36        12.46        12.59        12.59 
TCGA-LN-A4MR TCGA-LN-A7HW TCGA-LN-A7HX TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-RE-A7BO 
       13.22        12.00        12.23         5.06        16.31         7.00 
TCGA-V5-A7RC TCGA-VR-AA7I 
        3.42        15.91 

$`5Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.16        30.25        26.33        21.01        47.93        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-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.85         5.92 
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-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 
       13.15        15.35        12.59        13.25        12.62        12.49 
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-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        25.25        10.52        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
       12.26        33.11         7.82         8.02         7.59         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-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        2.30        12.69        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24         9.17        18.21 
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 TCGA-ZR-A9CJ 
        2.66        19.73 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.30              0.13 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            33.27            122.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           12.525            13.180 
[1] "0.3 - 33.3 (12.5)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         1        0        1        0         6         1
  5Q GAIN WILD-TYPE       7        5        5        1        41        30
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           3          1          0          3        0
  5Q GAIN WILD-TYPE        22         13          9          4        5
                   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                6                41
  STAGE IIB                1                30
  STAGE III                3                22
  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
  5Q GAIN MUTATED       2  3 11  1
  5Q GAIN WILD-TYPE    30 40 76  4
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               2                30
  T2                  3                40
  T3                 11                76
  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    9  4  1  3
  5Q GAIN WILD-TYPE 68 64 11  5
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               9                68
  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"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    13   0
  5Q GAIN WILD-TYPE 122   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     13    0
  5Q GAIN WILD-TYPE  122    9
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              13               122
  1               0                 9
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3  17
  5Q GAIN WILD-TYPE  24 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   17
  5Q GAIN WILD-TYPE   24  140
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               3                24
  MALE                17               140
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    15   4
  5Q GAIN WILD-TYPE 108  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     15    4
  5Q GAIN WILD-TYPE  108   39
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               15               108
  YES               4                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    12   2   1   1
  5Q GAIN WILD-TYPE 125  10   1   6
D10V12, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              12               125
  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"
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   19 20
  6P GAIN WILD-TYPE 89 56
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               39               145 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               20                56 
$`6P GAIN MUTATED`
TCGA-L5-A8NT TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM 
       27.12        25.78        31.27        14.30         7.63        13.94 
TCGA-2H-A9GO TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43E 
       16.24         3.88         4.67       122.10        68.02        30.25 
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
       47.93        58.59         7.13        15.48         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NQ 
        3.02        55.50         2.66        12.92         5.49        21.37 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ 
       10.85        10.36        10.45        13.15        12.62        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 
       12.00        12.23        13.18        16.31         7.04        15.78 
TCGA-VR-A8EQ TCGA-VR-AA7I TCGA-Z6-A8JE 
       22.82        15.91         2.10 

$`6P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ 
        5.16        20.02        58.55         5.92         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        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-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.79        23.41        12.82         9.96        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       12.16        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        32.61        21.01        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38         3.16         4.90        29.00         7.43 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       25.12         7.40        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         8.71        13.41        83.24        52.57        46.09 
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-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        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-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY 
       13.22         4.47        12.33        25.25        10.52        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.38         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35        53.95         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        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-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24         9.17        18.21 
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 
TCGA-ZR-A9CJ 
       19.73 

  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 
            13.15             12.85 
[1] "2.1 - 122.1 (13.2)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         3        1        1        0         8         6
  6P GAIN WILD-TYPE       5        4        5        1        39        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           8          1          2          1        1
  6P GAIN WILD-TYPE        17         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                8                39
  STAGE IIB                6                25
  STAGE III                8                17
  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  8 19  1
  6P GAIN WILD-TYPE    24 35 68  4
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1               8                24
  T2                  8                35
  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 16  2  1
  6P GAIN WILD-TYPE 60 52 10  7
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              17                60
  N1              16                52
  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    28   4
  6P GAIN WILD-TYPE 107   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     28    4
  6P GAIN WILD-TYPE  107    5
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              28               107
  1               4                 5
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6  33
  6P GAIN WILD-TYPE  21 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6   33
  6P GAIN WILD-TYPE   21  124
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               6                21
  MALE                33               124
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   27  9
  6P GAIN WILD-TYPE 96 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     27    9
  6P GAIN WILD-TYPE   96   34
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               27                96
  YES               9                34
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   24 15
  6P GAIN WILD-TYPE 64 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     24   15
  6P GAIN WILD-TYPE   64   81
                                   clus
vv                                  6P GAIN MUTATED 6P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  24                64
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              15                81
[1] 2 2
[1] FALSE
D11V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    30   3   1   1
  6P GAIN WILD-TYPE 107   9   1   6
D11V12, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              30               107
  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       9                         1    22
  6P GAIN WILD-TYPE    37                         4    92
D11V14, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   9                37
  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"
D11V15, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    0 15
  6P GAIN WILD-TYPE  6 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   15
  6P GAIN WILD-TYPE    6   73
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              15                73
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   16 17
  6Q GAIN WILD-TYPE 92 59
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               33               151 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17                59 
$`6Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A8NT TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM 
       60.39        27.12        31.27        14.30         7.63        13.94 
TCGA-2H-A9GO TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A4OW 
       16.24         3.88       122.10        68.02        30.25         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       15.48         2.60         3.02        55.50         2.66        12.92 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X 
       21.37        10.85        10.36        10.45        13.15        12.62 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A8I1 TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.33         4.47        12.23        13.18        16.31         7.04 
TCGA-R6-A8W5 TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.78        15.91         2.10 

$`6Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        35.97         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ 
       20.02        25.78        58.55         5.92         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        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-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       14.50        12.16        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16         0.30        26.33        32.61        21.01        47.93 
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-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        4.90        29.00         7.43        25.12         7.40         3.75 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
        8.71        13.41        83.24        52.57        46.09         5.92 
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-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-A4MR 
       12.59        22.39        12.85        15.52        11.54        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
       33.11         7.82         8.02         7.59         5.06        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24         9.17        18.21 
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 
TCGA-ZR-A9CJ 
       19.73 

  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 
            13.15             12.85 
[1] "2.1 - 122.1 (13.2)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.2"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         4        0        1        0         7         5
  6Q GAIN WILD-TYPE       4        5        5        1        40        26
                   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                7                40
  STAGE IIB                5                26
  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  6 15  1
  6Q GAIN WILD-TYPE    24 37 72  4
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               8                24
  T2                  6                37
  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
  6Q GAIN MUTATED   16 12  1  1
  6Q GAIN WILD-TYPE 61 56 11  7
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              16                61
  N1              12                56
  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     4  29
  6Q GAIN WILD-TYPE  23 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4   29
  6Q GAIN WILD-TYPE   23  128
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               4                23
  MALE                29               128
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   24  8
  6Q GAIN WILD-TYPE 99 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     24    8
  6Q GAIN WILD-TYPE   99   35
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               24                99
  YES               8                35
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   20 13
  6Q GAIN WILD-TYPE 68 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     20   13
  6Q GAIN WILD-TYPE   68   83
                                   clus
vv                                  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  20                68
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              13                83
[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       8                         1    18
  6Q GAIN WILD-TYPE    38                         4    96
D12V14, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   8                38
  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 14
  6Q GAIN WILD-TYPE  6 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   14
  6Q GAIN WILD-TYPE    6   74
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              14                74
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   68 41
  7P GAIN WILD-TYPE 40 35
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              109                75 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               41                35 
$`7P GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39         4.31        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       27.12        25.78         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       32.45         7.69        35.21         2.63        20.12        18.64 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A939 
        0.53        17.03         0.79        23.41        14.50        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       23.18        25.22         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       32.61        18.35         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
        4.90         7.13        15.48         2.60         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
        2.66        12.92        16.47        13.55        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41        13.38        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.62        12.59        12.49        12.76        12.59        12.85 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8HZ 
       12.33        13.22        12.33        25.25        12.00        12.33 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        12.85        12.26         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35         9.27         8.98        27.09         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I 
        8.12        28.11        33.70        46.19        11.24        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        25.08        14.37         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`7P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         8.94        19.99        22.82 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
        5.16        20.02        31.27        14.30        58.55         7.63 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT 
        4.21        33.27         0.85        20.78         3.88         9.30 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93D 
       44.75        68.02         3.68        41.52        47.38        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OU 
       24.03         6.28        21.01        47.93         7.17        29.00 
TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM 
        7.43        25.12         7.40        55.50        13.48         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P 
       21.37        13.41        83.24        10.45        12.66        12.33 
TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 
       13.15        12.46        22.39        15.52        11.54         4.47 
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-A9FP TCGA-M9-A5M8 TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-V5-A7RE 
       12.03        33.11         6.35        15.78         2.89        16.44 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       25.81        22.82        12.43        18.18        52.27        18.05 
TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A8JD 
        9.17        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             13.48 
[1] "0.1 - 60.4 (12.6)"  "0.8 - 122.1 (13.5)"
[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 98
  7P GAIN WILD-TYPE 16 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     11   98
  7P GAIN WILD-TYPE   16   59
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              11                16
  MALE                98                59
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   72 23
  7P GAIN WILD-TYPE 51 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     72   23
  7P GAIN WILD-TYPE   51   20
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               72                51
  YES              23                20
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   57 52
  7P GAIN WILD-TYPE 31 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     57   52
  7P GAIN WILD-TYPE   31   44
                                   clus
vv                                  7P GAIN MUTATED 7P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  57                31
  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    68
  7P GAIN WILD-TYPE    20                         0    46
D13V14, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                  26                20
  BLACK OR AFRICAN AMERICAN               5                 0
  WHITE                                  68                46
[1] 3 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 53
  7P GAIN WILD-TYPE  1 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5   53
  7P GAIN WILD-TYPE    1   35
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 1
  NOT HISPANIC OR LATINO              53                35
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   54 33
  7Q GAIN WILD-TYPE 54 43
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               87                97 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               33                43 
$`7Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39         4.31        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
       27.12         8.94        16.24        32.45         7.69        35.21 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A939 
       20.12        18.64        17.03        23.41        14.50        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        25.22         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT 
       26.33        32.61        47.93         3.32         3.16         4.90 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NL 
       15.48         2.60         3.75         3.02         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
        5.49        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 
       13.41        12.33        13.38        15.35        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.76        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FQ 
       12.33        25.25        12.00        12.33         0.13        12.85 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 
        7.82         8.02        16.31         7.04        38.40         9.30 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       15.35         9.27        27.09        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T6 
       33.70        18.18        46.19        11.24        18.21        25.08 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        2.10         1.32        19.73 

$`7Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         8.94        19.99        22.82 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        5.16        20.02        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 
        7.63         5.92        13.94         4.21        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.78         2.63         3.88         9.30         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93F 
       44.75        68.02         3.68        41.52        47.38        24.03 
TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        6.28        21.01        18.35         7.17         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE 
       29.00         7.13         7.43        25.12         7.40        55.50 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        8.71        13.41        83.24        10.45        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
       13.15        13.25        12.62        12.46        12.59        12.59 
TCGA-LN-A4A5 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       22.39         4.47        10.52        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DQ 
       13.38        13.18        12.03        12.26        33.11         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-V5-A7RE 
        5.06         6.35        53.95        15.78         2.89        16.44 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8Q7 
        8.98        25.81        22.82        12.43         1.55        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-AAPN 
        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 
            12.85             13.15 
[1] "0.1 - 60.4 (12.8)"  "0.5 - 122.1 (13.2)"
[1] "hr=" "1.1"
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           9          4          5          5        3
  7Q GAIN WILD-TYPE        16         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                9                16
  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 42  0
  7Q GAIN WILD-TYPE    13 28 45  5
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              19                13
  T2                 15                28
  T3                 42                45
  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 30  5  6
  7Q GAIN WILD-TYPE 43 38  7  2
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              34                43
  N1              30                38
  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   56  6
  7Q GAIN WILD-TYPE 79  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     56    6
  7Q GAIN WILD-TYPE   79    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              56                79
  1               6                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7 80
  7Q GAIN WILD-TYPE 20 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7   80
  7Q GAIN WILD-TYPE   20   77
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               7                20
  MALE                80                77
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   60 19
  7Q GAIN WILD-TYPE 63 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     60   19
  7Q GAIN WILD-TYPE   63   24
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               60                63
  YES              19                24
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   44 43
  7Q GAIN WILD-TYPE 44 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     44   43
  7Q GAIN WILD-TYPE   44   53
                                   clus
vv                                  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  44                44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              43                53
[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      22                         4    56
  7Q GAIN WILD-TYPE    24                         1    58
D14V14, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                  22                24
  BLACK OR AFRICAN AMERICAN               4                 1
  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"
D14V15, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4 43
  7Q GAIN WILD-TYPE  2 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4   43
  7Q GAIN WILD-TYPE    2   45
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 2
  NOT HISPANIC OR LATINO              43                45
[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 75 42
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               67               117 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               34                42 
$`8P GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-2H-A9GI 
       18.28         4.31        19.99         0.36        35.97        14.30 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD 
       20.78        17.03        12.82         4.67       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
        3.68        31.56        24.03         3.16        30.25         0.30 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
       47.93        18.35         1.38         3.16         4.90         7.13 
TCGA-L5-A88V TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS 
        2.60        13.55        13.22         7.76        21.37        13.41 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V 
       10.85         5.92        10.45        13.41        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-LN-A8HZ TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A8W5 
       12.33         0.13         7.59         5.06         7.04        15.78 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ 
       12.69         7.00        16.44        15.35        27.09        22.82 
TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-A8JE 
        8.12        18.18        46.19        11.24         3.42         2.10 
TCGA-ZR-A9CJ 
       19.73 

$`8P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH 
       22.82        27.12         5.16        20.02        25.78        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IG-A3Y9 
       58.55         7.63         5.92        13.94         7.69         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        0.79        23.41         9.96        14.86        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
       44.75        41.52        47.38        21.70        23.18        25.22 
TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
        6.28        26.33        32.61        21.01         3.32         7.17 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       58.59        29.00         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       16.47         5.49         8.71        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.36        12.66        12.43        12.33        13.38        13.15 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.46        12.59        12.49        12.76        22.39        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-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP 
       10.52        12.00        12.23        13.38        13.18        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 
       12.85        12.26        33.11         7.82         8.02        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35        53.95         9.30         2.89         2.30 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.38         5.29         3.42         9.27         8.98        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-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       14.37         1.32         2.66 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.13              0.53 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           122.10             83.24 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            12.85             13.15 
[1] "0.1 - 122.1 (12.8)" "0.5 - 83.2 (13.2)" 
[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          4        2
  8P GAIN WILD-TYPE        13         10          5          3        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               4                 3
  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 12 38  1
  8P GAIN WILD-TYPE    22 31 49  4
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              10                22
  T2                 12                31
  T3                 38                49
  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  5
  8P GAIN WILD-TYPE 49 45  7  3
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              28                49
  N1              23                45
  N2               5                 7
  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"
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  57
  8P GAIN WILD-TYPE  17 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     10   57
  8P GAIN WILD-TYPE   17  100
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              10                17
  MALE                57               100
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   43 16
  8P GAIN WILD-TYPE 80 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     43   16
  8P GAIN WILD-TYPE   80   27
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               43                80
  YES              16                27
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   32 35
  8P GAIN WILD-TYPE 56 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     32   35
  8P GAIN WILD-TYPE   56   61
                                   clus
vv                                  8P GAIN MUTATED 8P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  32                56
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              35                61
[1] 2 2
[1] FALSE
D15V11, continuous
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED   48  7  0  3
  8P GAIN WILD-TYPE 89  5  2  4
D15V12, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              48                89
  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    42
  8P GAIN WILD-TYPE    29                         3    72
D15V14, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                  17                29
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  42                72
[1] 3 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 29
  8P GAIN WILD-TYPE  5 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   29
  8P GAIN WILD-TYPE    5   59
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              29                59
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   60 42
  8Q GAIN WILD-TYPE 48 34
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              102                82 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               42                34 
$`8Q GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       18.28         4.31        19.99         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       20.02        14.30        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27        35.21        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H 
       20.12         3.88        17.03        12.82         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
      122.10        68.02         3.68        23.18        31.56        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.16        30.25         0.30        47.93        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        1.38         3.16         4.90         7.13         7.43         2.60 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       13.41        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.62        12.46        12.59        12.59        12.85        11.54 
TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.33        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
        0.13        12.85        12.26         7.59         5.06         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
       53.95        15.78        12.69         7.00        20.38        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        27.09        22.82        12.43 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
        8.12        33.70        18.18        46.19        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       15.91        41.23         3.42         2.10         1.32        19.73 

$`8Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       22.82         5.16        25.78        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
        5.92         0.85        18.64         9.30         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FG 
       23.41         9.96        14.86        12.16        44.75        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OH 
       47.38        21.70        25.22         6.28        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88W 
       21.01         7.17        58.59        29.00        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49N 
       13.48        16.47        83.24        52.57        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       13.15        12.49        12.76        22.39        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A8I0 
       13.22         4.47        25.25        10.52        12.00        13.38 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG 
       12.03        33.11         7.82         8.02        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC 
        6.35         9.30         2.89         2.30         5.29         3.42 
TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G 
       25.81         1.55        18.31        28.11        52.27        18.05 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       18.21        25.08        14.37         2.66 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.13              0.53 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           122.10             83.24 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           12.655            13.925 
[1] "0.1 - 122.1 (12.7)" "0.5 - 83.2 (13.9)" 
[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        25        16
  8Q GAIN WILD-TYPE       6        3        2        0        22        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          17          8          6          7        2
  8Q GAIN WILD-TYPE         8          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               25                22
  STAGE IIB               16                15
  STAGE III               17                 8
  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 21 57  3
  8Q GAIN WILD-TYPE    20 22 30  2
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              12                20
  T2                 21                22
  T3                 57                30
  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   40 37  7  8
  8Q GAIN WILD-TYPE 37 31  5  0
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              40                37
  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   75  4
  8Q GAIN WILD-TYPE 60  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     75    4
  8Q GAIN WILD-TYPE   60    5
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              75                60
  1               4                 5
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   14 88
  8Q GAIN WILD-TYPE 13 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14   88
  8Q GAIN WILD-TYPE   13   69
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              14                13
  MALE                88                69
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   63 28
  8Q GAIN WILD-TYPE 60 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     63   28
  8Q GAIN WILD-TYPE   60   15
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               63                60
  YES              28                15
[1] 2 2
[1] FALSE
D16V9, continuous
D16V10, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   47 55
  8Q GAIN WILD-TYPE 41 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     47   55
  8Q GAIN WILD-TYPE   41   41
                                   clus
vv                                  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  47                41
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              55                41
[1] 2 2
[1] FALSE
D16V11, continuous
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   76  9  1  3
  8Q GAIN WILD-TYPE 61  3  1  4
D16V12, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              76                61
  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      29                         2    61
  8Q GAIN WILD-TYPE    17                         3    53
D16V14, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                  29                17
  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 51
  8Q GAIN WILD-TYPE  4 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2   51
  8Q GAIN WILD-TYPE    4   37
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              51                37
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED   13  4
  9P GAIN WILD-TYPE 95 72
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               167 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                72 
$`9P GAIN MUTATED`
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-2H-A9GL TCGA-IG-A625 TCGA-JY-A6F8 TCGA-L5-A4OU 
        0.36        27.12         5.92        12.82       122.10        29.00 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V 
       10.85        10.36        13.41        12.33        13.38        12.59 
TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-VR-AA4G TCGA-VR-AA7D TCGA-Z6-AAPN 
       13.38        12.85        18.05         9.17         2.66 

$`9P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU 
       24.00         4.70        19.99        22.82        35.97         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        31.27        14.30        58.55         7.63 
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-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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
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-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
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-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        12.33        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.26        33.11         7.82         8.02         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-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-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         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-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       46.19        11.24        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32        19.73 

  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 
            12.82             13.18 
[1] "0.4 - 122.1 (12.8)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.8"
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          2        0
  9P GAIN WILD-TYPE        23         13          8          5        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               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
  9P GAIN MUTATED       2  2 12  0
  9P GAIN WILD-TYPE    30 41 75  5
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               2                30
  T2                  2                41
  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
  9P GAIN MUTATED   10  2  2  2
  9P GAIN WILD-TYPE 67 66 10  6
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              10                67
  N1               2                66
  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"
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  16
  9P GAIN WILD-TYPE  26 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   16
  9P GAIN WILD-TYPE   26  141
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               1                26
  MALE                16               141
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     7   8
  9P GAIN WILD-TYPE 116  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      7    8
  9P GAIN WILD-TYPE  116   35
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                7               116
  YES               8                35
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    6 11
  9P GAIN WILD-TYPE 82 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6   11
  9P GAIN WILD-TYPE   82   85
                                   clus
vv                                  9P GAIN MUTATED 9P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   6                82
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              11                85
[1] 2 2
[1] FALSE
D17V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    14   2   0   0
  9P GAIN WILD-TYPE 123  10   2   7
D17V12, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              14               123
  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     7
  9P GAIN WILD-TYPE    39                         4   107
D17V14, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   7                39
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   7               107
[1] 3 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 10
  9P GAIN WILD-TYPE  6 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   10
  9P GAIN WILD-TYPE    6   78
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              10                78
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   24 10
  9Q GAIN WILD-TYPE 84 66
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               34               150 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10                66 
$`9Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GL TCGA-IC-A6RE 
       60.39         0.36        27.12        20.02         5.92         7.69 
TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OU 
        0.53        12.82       122.10         3.16         3.32        29.00 
TCGA-L5-A8NL TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P 
       13.22        10.85        10.36         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-R6-A6L4 TCGA-VR-A8ER 
        4.47        13.38        12.85        12.26        16.31        12.43 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-Z6-AAPN 
       18.05         9.17        25.08         2.66 

$`9Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-2H-A9GF 
        4.70        19.99        22.82        35.97         5.16        25.78 
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-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         9.96        14.86         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-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L 
        8.71        13.41        83.24        52.57        46.09        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y 
       12.66        12.43        13.15        15.35        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.76        12.59        22.39        12.85        15.52 
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-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.18         0.13        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
       33.11         7.82         8.02         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-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       18.18        52.27        46.19        11.24        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         1.32        19.73 

  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 
            12.46             13.33 
[1] "0.4 - 122.1 (12.5)" "0.1 - 83.2 (13.3)" 
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         2        0        0        0        11         4
  9Q GAIN WILD-TYPE       6        5        6        1        36        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           5          3          1          3        1
  9Q GAIN WILD-TYPE        20         11          8          4        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                4                27
  STAGE III                5                20
  STAGE IIIA               3                11
  STAGE IIIB               1                 8
  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
  9Q GAIN MUTATED       4  5 21  1
  9Q GAIN WILD-TYPE    28 38 66  4
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               4                28
  T2                  5                38
  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
  9Q GAIN MUTATED   15 11  2  3
  9Q GAIN WILD-TYPE 62 57 10  5
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              15                62
  N1              11                57
  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"
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  33
  9Q GAIN WILD-TYPE  26 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   33
  9Q GAIN WILD-TYPE   26  124
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               1                26
  MALE                33               124
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    17  12
  9Q GAIN WILD-TYPE 106  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     17   12
  9Q GAIN WILD-TYPE  106   31
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               17               106
  YES              12                31
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   13 21
  9Q GAIN WILD-TYPE 75 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     13   21
  9Q GAIN WILD-TYPE   75   75
                                   clus
vv                                  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  13                75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              21                75
[1] 2 2
[1] FALSE
D18V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    28   3   1   0
  9Q GAIN WILD-TYPE 109   9   1   7
D18V12, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              28               109
  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    14
  9Q GAIN WILD-TYPE    31                         3   100
D18V14, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                  15                31
  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"
D18V15, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1 21
  9Q GAIN WILD-TYPE  5 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   21
  9Q GAIN WILD-TYPE    5   67
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              21                67
[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 83 61
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                40                144 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                15                 61 
$`10P GAIN MUTATED`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR 
       15.68        18.28        58.55        13.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3YC TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OH 
        7.69        20.12       122.10        25.22         3.16        32.61 
TCGA-L5-A4OR TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.16         2.60         3.02        55.50        12.92        16.47 
TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A4A1 
        8.71        10.36        10.45        13.38        13.15        12.59 
TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ 
       12.85        12.33        12.23         8.02         5.06         6.35 
TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8Q7 
       15.78        20.38         9.27         1.55        18.31        52.27 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-A9VB 
       46.19        18.21         2.10         1.32 

$`10P GAIN WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL 
       20.02        25.78        31.27        14.30         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94         4.21        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         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-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        21.01        47.93        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-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43        15.48        25.12         7.40         3.75 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37        13.41        83.24        52.57        46.09        10.85 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U 
        5.92        12.66        12.43        13.41        12.33        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        25.25        10.52        12.00        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         7.82         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       38.40        53.95         9.30         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        7.00         5.29         3.42        16.44        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX 
       25.81        27.09        22.82        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 TCGA-ZR-A9CJ 
       25.08        41.23        14.37         3.42         2.66        19.73 

  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             13.015 
[1] "1.3 - 122.1 (13.0)" "0.1 - 83.2 (13.0)" 
[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 95 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     28   10
  10P GAIN WILD-TYPE   95   33
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                28                 95
  YES               10                 33
[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   17 14
  10Q GAIN WILD-TYPE 91 62
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                31                153 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                 62 
$`10Q GAIN MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE 
       15.68         4.31        58.55        13.94        16.24         7.69 
TCGA-IG-A3YC TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A4OH TCGA-L5-A4OR 
       20.12         0.79       122.10        25.22        32.61         3.16 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L 
        3.02        55.50        12.92        16.47        10.36        10.45 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A9FQ TCGA-R6-A6DN TCGA-R6-A6KZ 
       13.15        12.59        12.59        12.85         8.02         5.06 
TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-X8-AAAR 
        6.35        15.78        20.38        22.82        52.27        18.21 
TCGA-ZR-A9CJ 
       19.73 

$`10Q GAIN WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL 
       20.02        25.78        31.27        14.30         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         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-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        7.40         3.75         2.66        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.85         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       13.41        12.33        13.38        15.35        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.03        12.26 
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-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-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        46.19        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 
             13.94              12.82 
[1] "0.8 - 122.1 (13.9)" "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          3          0          2        1
  10Q GAIN WILD-TYPE        23         11          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                3                 11
  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 15  0
  10Q GAIN WILD-TYPE    22 40 72  5
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1               10                 22
  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
  10Q GAIN MUTATED   15 11  0  2
  10Q GAIN WILD-TYPE 62 57 12  6
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               15                 62
  N1               11                 57
  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    19   3
  10Q GAIN WILD-TYPE 116   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     19    3
  10Q GAIN WILD-TYPE  116    6
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               19                116
  1                3                  6
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  29
  10Q GAIN WILD-TYPE  25 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   29
  10Q GAIN WILD-TYPE   25  128
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                 29                128
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    23   5
  10Q GAIN WILD-TYPE 100  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     23    5
  10Q GAIN WILD-TYPE  100   38
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                23                100
  YES                5                 38
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   20 11
  10Q GAIN WILD-TYPE 68 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     20   11
  10Q GAIN WILD-TYPE   68   85
                                   clus
vv                                  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   20                 68
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               11                 85
[1] 2 2
[1] FALSE
D20V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    23   1   0   1
  10Q GAIN WILD-TYPE 114  11   2   6
D20V12, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               23                114
  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    23
  10Q GAIN WILD-TYPE    41                         5    91
D20V14, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    5                 41
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                   23                 91
[1] 3 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 17
  10Q GAIN WILD-TYPE  6 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   17
  10Q GAIN WILD-TYPE    6   71
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               17                 71
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED   18 21
  11P GAIN WILD-TYPE 90 55
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                39                145 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                21                 55 
$`11P GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A8NT TCGA-2H-A9GN TCGA-2H-A9GO 
       60.39         8.94        24.00        27.12         8.94        16.24 
TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-L5-A4OF TCGA-L5-A4OM 
       23.41        14.50       122.10         3.68        26.33        47.93 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW 
        1.38        29.00         2.66         5.49        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR 
        5.92        12.33        12.59        12.46        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ 
        4.47        12.33        13.38        12.26         7.82         7.59 
TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY 
        7.04         7.00         3.42        22.82         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-AA7I TCGA-ZR-A9CJ 
       18.18        15.91        19.73 

$`11P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        34.85        18.28         4.31         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82         0.36        35.97         5.16        20.02        25.78 
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-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
        4.67        12.16        44.75        68.02        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON 
        3.16        30.25         0.30        32.61        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        3.32         7.17         3.16        58.59         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76        21.37         8.71        13.41        83.24 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.38        13.15        15.35        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-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       11.54        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.03        13.18        13.18         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         8.02         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-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       25.81        27.09        12.43         1.55        18.31        28.11 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24         9.17        18.21 
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 
             12.59              13.15 
[1] "1.4 - 122.1 (12.6)" "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        11         5
  11P GAIN WILD-TYPE       6        4        5        1        36        26
                    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                11                 36
  STAGE IIB                 5                 26
  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       6  6 23  1
  11P GAIN WILD-TYPE    26 37 64  4
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                6                 26
  T2                   6                 37
  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   17 11  5  2
  11P GAIN WILD-TYPE 60 57  7  6
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               17                 60
  N1               11                 57
  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    27   3
  11P GAIN WILD-TYPE 108   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     27    3
  11P GAIN WILD-TYPE  108    6
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               27                108
  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  7
  11P GAIN WILD-TYPE 93 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     30    7
  11P GAIN WILD-TYPE   93   36
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                30                 93
  YES                7                 36
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, binary
                    cls
clus                  0  1
  11P GAIN MUTATED   20 19
  11P GAIN WILD-TYPE 68 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     20   19
  11P GAIN WILD-TYPE   68   77
                                   clus
vv                                  11P GAIN MUTATED 11P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   20                 68
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               19                 77
[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      12                         1    23
  11P GAIN WILD-TYPE    34                         4    91
D21V14, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                   12                 34
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   23                 91
[1] 3 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 18
  11P GAIN WILD-TYPE  6 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   18
  11P GAIN WILD-TYPE    6   70
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               18                 70
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED   17 12
  11Q GAIN WILD-TYPE 91 64
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                155 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                 64 
$`11Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A88Y TCGA-IG-A51D TCGA-IG-A97H 
       60.39         8.94        24.00         0.36        17.03        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OQ TCGA-L5-A4OU 
      122.10         3.68        26.33        32.61         1.38        29.00 
TCGA-L5-A8NN TCGA-LN-A49K TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A8I0 
        5.49         5.92        12.46        12.33        13.22        13.38 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-RE-A7BO 
       12.26         7.82         7.59         7.04        15.78         7.00 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-ZR-A9CJ 
        9.27        22.82         8.12        33.70        19.73 

$`11Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        34.85        18.28         4.31         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82        35.97        27.12         5.16        20.02        25.78 
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-A3I8 
        8.94        16.24         4.21        32.45         7.69        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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86         4.67        12.16        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ 
       24.03         6.28         3.16        30.25         0.30        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36        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-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-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        11.54         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.13        12.03        12.85        33.11         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       16.31        38.40         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31        28.11        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        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 

  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 
             12.46              13.15 
[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         7         4
  11Q GAIN WILD-TYPE       5        5        6        1        40        27
                    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                 7                 40
  STAGE IIB                 4                 27
  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       7  4 15  0
  11Q GAIN WILD-TYPE    25 39 72  5
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                7                 25
  T2                   4                 39
  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   10  9  5  1
  11Q GAIN WILD-TYPE 67 59  7  7
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               10                 67
  N1                9                 59
  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    19   1
  11Q GAIN WILD-TYPE 116   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     19    1
  11Q GAIN WILD-TYPE  116    8
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               19                116
  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    23   3
  11Q GAIN WILD-TYPE 100  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     23    3
  11Q GAIN WILD-TYPE  100   40
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                23                100
  YES                3                 40
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   18 11
  11Q GAIN WILD-TYPE 70 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     18   11
  11Q GAIN WILD-TYPE   70   85
                                   clus
vv                                  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   18                 70
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               11                 85
[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       8                         0    20
  11Q GAIN WILD-TYPE    38                         5    94
D22V14, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    8                 38
  BLACK OR AFRICAN AMERICAN                0                  5
  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"
D22V15, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    0 15
  11Q GAIN WILD-TYPE  6 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   15
  11Q GAIN WILD-TYPE    6   73
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               15                 73
[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 73 54
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                57                127 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                22                 54 
$`12P GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NT TCGA-2H-A9GK 
        4.31        24.00        19.99         0.36        27.12         7.63 
TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5S3 
       16.24        35.21         2.63        18.64         0.53        23.41 
TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A8NF 
        4.67         0.30        47.93         3.32         4.90         2.66 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.22         5.49        21.37        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       10.45        12.33        13.38        13.15        12.59        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR 
       12.59        12.76        12.59        12.85        15.52        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
        4.47        12.33        25.25        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WG 
        0.13         8.02         7.59        38.40        53.95        12.69 
TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       20.38        27.09         1.55        18.31         8.12        28.11 
TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       14.37         1.32         2.66 

$`12P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         8.94         4.70 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH 
       22.82        35.97         5.16        20.02        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       14.30        58.55         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
       32.45         7.69        33.27         0.85        20.78        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       32.61        21.01        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
       25.12         7.40         3.75         3.02        55.50        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        16.47        13.55         7.76         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        46.09        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-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ 
       12.03        12.85        12.26        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-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        2.30         7.00         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EY 
        9.27         8.98        25.81        22.82        12.43        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23         3.42         2.10 
TCGA-ZR-A9CJ 
       19.73 

  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 
             12.59              13.48 
[1] "0.1 - 54.0 (12.6)"  "0.8 - 122.1 (13.5)"
[1] "hr=" "1.3"
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          3          4          3        3
  12P GAIN WILD-TYPE        17         11          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                3                 11
  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 30  0
  12P GAIN WILD-TYPE    26 28 57  5
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1                6                 26
  T2                  15                 28
  T3                  30                 57
  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 19  4  3
  12P GAIN WILD-TYPE 52 49  8  5
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               25                 52
  N1               19                 49
  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   38  6
  12P GAIN WILD-TYPE 97  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     38    6
  12P GAIN WILD-TYPE   97    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               38                 97
  1                6                  3
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     4  53
  12P GAIN WILD-TYPE  23 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4   53
  12P GAIN WILD-TYPE   23  104
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                4                 23
  MALE                 53                104
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   31 18
  12P GAIN WILD-TYPE 92 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     31   18
  12P GAIN WILD-TYPE   92   25
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                31                 92
  YES               18                 25
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   17 40
  12P GAIN WILD-TYPE 71 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     17   40
  12P GAIN WILD-TYPE   71   56
                                   clus
vv                                  12P GAIN MUTATED 12P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   17                 71
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               40                 56
[1] 2 2
[1] FALSE
D23V11, continuous
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED   41  4  1  2
  12P GAIN WILD-TYPE 96  8  1  5
D23V12, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               41                 96
  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    29
  12P GAIN WILD-TYPE    23                         3    85
D23V14, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                   23                 23
  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"
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 86 61
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                37                147 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                 61 
$`12Q GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A88Y TCGA-L5-A8NT TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3YB 
       24.00         0.36        27.12         7.63        16.24         2.63 
TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A8NL 
        0.53         4.67        47.93         3.32         4.90        13.22 
TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A49W 
        5.49        52.57        10.36        10.45        12.59        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.59        12.85        15.52        11.54        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-R6-A6DQ 
       12.33        25.25        12.33        13.18         0.13         7.59 
TCGA-R6-A6XG TCGA-R6-A8WG TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EX TCGA-Z6-AAPN 
       38.40        12.69        27.09        18.31        28.11         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`12Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        19.99        22.82        35.97         5.16        20.02 
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-A3I8 TCGA-IG-A3QL 
        8.94         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       32.61        21.01        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
        8.71        13.41        83.24        46.09        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-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       15.35        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       22.39        13.22        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18        13.38        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.82         8.02         5.06        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-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
        8.98        25.81        22.82        12.43         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
        3.42         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              13.38 
[1] "0.1 - 52.6 (12.6)"  "0.3 - 122.1 (13.4)"
[1] "hr=" "1.2"
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          2          3          3        3
  12Q GAIN WILD-TYPE        20         12          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                2                 12
  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 21  0
  12Q GAIN WILD-TYPE    28 34 66  5
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                4                 28
  T2                   9                 34
  T3                  21                 66
  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 13  3  3
  12Q GAIN WILD-TYPE 62 55  9  5
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               15                 62
  N1               13                 55
  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    24   5
  12Q GAIN WILD-TYPE 111   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     24    5
  12Q GAIN WILD-TYPE  111    4
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               24                111
  1                5                  4
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3  34
  12Q GAIN WILD-TYPE  24 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   34
  12Q GAIN WILD-TYPE   24  123
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 34                123
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    21  10
  12Q GAIN WILD-TYPE 102  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     21   10
  12Q GAIN WILD-TYPE  102   33
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                21                102
  YES               10                 33
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   15 22
  12Q GAIN WILD-TYPE 73 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     15   22
  12Q GAIN WILD-TYPE   73   74
                                   clus
vv                                  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   15                 73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               22                 74
[1] 2 2
[1] FALSE
D24V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    27   3   1   1
  12Q GAIN WILD-TYPE 110   9   1   6
D24V12, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               27                110
  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    18
  12Q GAIN WILD-TYPE    30                         5    96
D24V14, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                   16                 30
  BLACK OR AFRICAN AMERICAN                0                  5
  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"
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   23 21
  13Q GAIN WILD-TYPE 85 55
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                44                140 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                 55 
$`13Q GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NT 
       18.28         8.94         4.70        19.99         0.36        27.12 
TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A5B8 
       20.02        31.27        14.30         5.92        13.94         0.79 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D 
       14.50       122.10         3.68        47.38        23.18        31.56 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A88V 
        3.16        30.25         7.17         1.38         7.13         2.60 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NR TCGA-LN-A4MQ TCGA-LN-A5U7 
        3.02         2.66        12.92         8.71        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 
       12.00        12.85         7.82        16.31         7.04         9.30 
TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-AA4D TCGA-X8-AAAR 
       15.78         5.29         3.42         9.27        46.19        18.21 
TCGA-XP-A8T6 TCGA-ZR-A9CJ 
       25.08        19.73 

$`13Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A88T 
       15.68        60.39        34.85         4.31        24.00        22.82 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN 
       35.97         5.16        25.78        58.55         7.63         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
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-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
       14.86         4.67        12.16        44.75        68.02        41.52 
TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF 
       21.70        25.22        24.03         6.28         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
       32.61        21.01        47.93        18.35         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W 
       58.59         4.90        29.00         7.43        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         3.75        55.50        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         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-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX 
       11.54        13.22         4.47        12.33        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        12.26        33.11         8.02         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       38.40         6.35        53.95         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        7.00        20.38        16.44        15.35         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        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 
             12.59              13.18 
[1] "0.4 - 122.1 (12.6)" "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           6          3          2          3        1
  13Q GAIN WILD-TYPE        19         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                 6                 19
  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 18  0
  13Q GAIN WILD-TYPE    19 36 69  5
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               13                 19
  T2                   7                 36
  T3                  18                 69
  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 17  4  3
  13Q GAIN WILD-TYPE 64 51  8  5
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               13                 64
  N1               17                 51
  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    24   3
  13Q GAIN WILD-TYPE 111   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     24    3
  13Q GAIN WILD-TYPE  111    6
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               24                111
  1                3                  6
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     6  38
  13Q GAIN WILD-TYPE  21 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   38
  13Q GAIN WILD-TYPE   21  119
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                6                 21
  MALE                 38                119
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   34  6
  13Q GAIN WILD-TYPE 89 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     34    6
  13Q GAIN WILD-TYPE   89   37
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                34                 89
  YES                6                 37
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   35  9
  13Q GAIN WILD-TYPE 53 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     35    9
  13Q GAIN WILD-TYPE   53   87
                                   clus
vv                                  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   35                 53
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                9                 87
[1] 2 2
[1] FALSE
D25V11, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    31   3   0   2
  13Q GAIN WILD-TYPE 106   9   2   5
D25V12, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               31                106
  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   31 18
  14Q GAIN WILD-TYPE 77 58
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                49                135 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                18                 58 
$`14Q GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A8NG TCGA-S8-A6BV TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.31        35.97        20.02         5.92         0.85        20.78 
TCGA-IG-A4P3 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FG TCGA-JY-A93C TCGA-L5-A43C 
       18.64         9.96        12.16        41.52        23.18         3.16 
TCGA-L5-A43E TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS 
       30.25         3.16         7.43         5.49        21.37        13.41 
TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 
        5.92        13.15        15.35        12.59        12.62        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY 
       12.59        11.54        13.22        12.33        25.25        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-R6-A6DN 
       13.18        12.33         0.13        12.03        12.26         8.02 
TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA7B 
       53.95        20.38         8.98         8.12        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
        9.17        15.91        25.08         3.42         2.10         1.32 
TCGA-ZR-A9CJ 
       19.73 

$`14Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
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-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       35.21         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41        12.82        14.86         4.67 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       14.50       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H 
       21.70        31.56        25.22        24.03         6.28         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22         7.76         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.33        13.38        13.25        12.46        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HV 
       22.39        12.85        15.52        12.33         4.47        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-M9-A5M8 
       12.00        12.23        13.38        13.18        12.85        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00         5.29         3.42        16.44        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-X8-AAAR 
       28.11        33.70        18.18        52.27        18.05        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       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 
             12.33              13.38 
[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           7          5          2          2        1
  14Q GAIN WILD-TYPE        18          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                 7                 18
  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 23  3
  14Q GAIN WILD-TYPE    29 27 64  2
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                3                 29
  T2                  16                 27
  T3                  23                 64
  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 16  2  3
  14Q GAIN WILD-TYPE 53 52 10  5
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               24                 53
  N1               16                 52
  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   39  1
  14Q GAIN WILD-TYPE 96  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     39    1
  14Q GAIN WILD-TYPE   96    8
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               39                 96
  1                1                  8
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  47
  14Q GAIN WILD-TYPE  25 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   47
  14Q GAIN WILD-TYPE   25  110
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                 47                110
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   32 14
  14Q GAIN WILD-TYPE 91 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     32   14
  14Q GAIN WILD-TYPE   91   29
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                32                 91
  YES               14                 29
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   15 34
  14Q GAIN WILD-TYPE 73 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   34
  14Q GAIN WILD-TYPE   73   62
                                   clus
vv                                  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   15                 73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               34                 62
[1] 2 2
[1] FALSE
D26V11, continuous
                    vv
clus                 R0 R1 R2 RX
  14Q GAIN MUTATED   40  1  1  2
  14Q GAIN WILD-TYPE 97 11  1  5
D26V12, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               40                 97
  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    27
  14Q GAIN WILD-TYPE    27                         4    87
D26V14, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                   19                 27
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   27                 87
[1] 3 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   17 14
  15Q GAIN WILD-TYPE 91 62
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                31                153 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                 62 
$`15Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A50L TCGA-JY-A6F8 
       60.39         0.36         7.63         8.94         0.53       122.10 
TCGA-L5-A43C TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A8NJ 
        3.16         3.16         7.13        15.48         2.60        16.47 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4MR TCGA-LN-A7HW 
       46.09        10.85        10.45        13.38        13.22        12.00 
TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 
       12.23        12.33        33.11         7.82         7.59         7.04 
TCGA-R6-A6XQ TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-AA7D TCGA-XP-A8T6 
        6.35        27.09        22.82         1.55         9.17        25.08 
TCGA-XP-A8T7 
       41.23 

$`15Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL 
       20.02        25.78        31.27        14.30        58.55         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94        16.24         4.21        32.45         7.69        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-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38        58.59         4.90        29.00         7.43 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ 
       21.37         8.71        13.41        83.24        52.57        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
        5.92        12.66        12.43        13.41        12.33        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-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33         4.47        12.33        25.25        10.52 
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-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
       12.85        12.26         8.02         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-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        9.27         8.98        25.81        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24        15.91        18.21        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  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 
             10.85              13.22 
[1] "0.4 - 122.1 (10.8)" "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         2
  15Q GAIN WILD-TYPE       6        4        4        1        39        29
                    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                 2                 29
  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 10 12  0
  15Q GAIN WILD-TYPE    28 33 75  5
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1                4                 28
  T2                  10                 33
  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 10  2  1
  15Q GAIN WILD-TYPE 64 58 10  7
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               13                 64
  N1               10                 58
  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    22   0
  15Q GAIN WILD-TYPE 113   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     22    0
  15Q GAIN WILD-TYPE  113    9
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               22                113
  1                0                  9
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3  28
  15Q GAIN WILD-TYPE  24 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   28
  15Q GAIN WILD-TYPE   24  129
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 28                129
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    21   7
  15Q GAIN WILD-TYPE 102  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     21    7
  15Q GAIN WILD-TYPE  102   36
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                21                102
  YES                7                 36
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   17 14
  15Q GAIN WILD-TYPE 71 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     17   14
  15Q GAIN WILD-TYPE   71   82
                                   clus
vv                                  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   17                 71
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               14                 82
[1] 2 2
[1] FALSE
D27V11, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    26   0   0   1
  15Q GAIN WILD-TYPE 111  12   2   6
D27V12, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               26                111
  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                         2    17
  15Q GAIN WILD-TYPE    39                         3    97
D27V14, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    7                 39
  BLACK OR AFRICAN AMERICAN                2                  3
  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    2 12
  15Q GAIN WILD-TYPE  4 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   12
  15Q GAIN WILD-TYPE    4   76
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  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 15
  16P GAIN WILD-TYPE 83 61
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                40                144 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                 61 
$`16P GAIN MUTATED`
TCGA-L5-A8NT TCGA-2H-A9GJ TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A8O2 
       27.12        58.55         0.85         0.53         0.79         4.67 
TCGA-IG-A97H TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NE 
       14.50         0.30         3.32        29.00        15.48        55.50 
TCGA-L5-A8NF TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49S 
        2.66        21.37        13.41        10.36         5.92        13.15 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR 
       13.25        12.59        12.76        12.85        11.54        13.22 
TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6KZ 
       12.33        12.03        13.18         0.13        12.85         5.06 
TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8EW 
       38.40        15.78        20.38        15.35        12.43         8.12 
TCGA-VR-A8EX TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       28.11        14.37         3.42        19.73 

$`16P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK 
        5.16        20.02        25.78        31.27        14.30         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27        35.21        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
       18.64         3.88         9.30        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        3.16        58.59         4.90         7.13         7.43         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.75         3.02        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76         5.49         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        46.09        10.85        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.38        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.62        12.46        12.49        12.59        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33         4.47        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18        12.33        13.38        12.03        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.82         8.02         7.59        16.31         7.04         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-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ 
       27.09        22.82         1.55        18.31        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        25.08        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              13.20 
[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        11         7
  16P GAIN WILD-TYPE       7        5        3        0        36        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           5          2          2          3        0
  16P GAIN WILD-TYPE        20         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                11                 36
  STAGE IIB                 7                 24
  STAGE III                 5                 20
  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 23  2
  16P GAIN WILD-TYPE    28 34 64  3
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                4                 28
  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
  16P GAIN MUTATED   21 11  2  3
  16P GAIN WILD-TYPE 56 57 10  5
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               21                 56
  N1               11                 57
  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    30   3
  16P GAIN WILD-TYPE 105   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     30    3
  16P GAIN WILD-TYPE  105    6
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               30                105
  1                3                  6
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  39
  16P GAIN WILD-TYPE  26 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   39
  16P GAIN WILD-TYPE   26  118
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                1                 26
  MALE                 39                118
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   25 11
  16P GAIN WILD-TYPE 98 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     25   11
  16P GAIN WILD-TYPE   98   32
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                25                 98
  YES               11                 32
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   12 28
  16P GAIN WILD-TYPE 76 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12   28
  16P GAIN WILD-TYPE   76   68
                                   clus
vv                                  16P GAIN MUTATED 16P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   12                 76
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               28                 68
[1] 2 2
[1] FALSE
D28V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    32   3   0   0
  16P GAIN WILD-TYPE 105   9   2   7
D28V12, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               32                105
  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                         2    18
  16P GAIN WILD-TYPE    29                         3    96
D28V14, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                   17                 29
  BLACK OR AFRICAN AMERICAN                2                  3
  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    1 25
  16P GAIN WILD-TYPE  5 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   25
  16P GAIN WILD-TYPE    5   63
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  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   21 17
  16Q GAIN WILD-TYPE 87 59
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                38                146 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                 59 
$`16Q GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A8NT TCGA-2H-A9GM TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-IG-A8O2 
        4.31        27.12        13.94         0.85         0.79         4.67 
TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NF TCGA-L5-A8NH 
        0.30         3.32        29.00        15.48         2.66        12.92 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49R TCGA-LN-A4A1 TCGA-LN-A4A3 
       21.37        13.41        52.57        13.38        12.59        12.76 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.85        11.54        12.33        12.03        13.18         0.13 
TCGA-LN-A9FQ TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       12.85        38.40        15.78        20.38         3.42        15.35 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA7B TCGA-XP-A8T8 TCGA-Z6-A8JD 
       12.43         8.12        28.11        11.24        14.37         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

$`16Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        35.97         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        5.92         8.94        16.24         4.21        32.45         7.69 
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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        83.24        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       10.45        12.66        12.43        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.46        12.49 
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-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.38        12.03        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
        9.30         2.89         2.30        12.69         7.00         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55        18.31        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         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 
            12.805             13.220 
[1] "0.1 - 52.6 (12.8)"  "0.4 - 122.1 (13.2)"
[1] "hr=" "1.6"
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           5          2          2          2        2
  16Q GAIN WILD-TYPE        20         12          7          5        3
                    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                 5                 20
  STAGE IIIA                2                 12
  STAGE IIIB                2                  7
  STAGE IIIC                2                  5
  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
  16Q GAIN MUTATED       5  7 22  2
  16Q GAIN WILD-TYPE    27 36 65  3
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                5                 27
  T2                   7                 36
  T3                  22                 65
  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   20 11  2  3
  16Q GAIN WILD-TYPE 57 57 10  5
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               20                 57
  N1               11                 57
  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    26   5
  16Q GAIN WILD-TYPE 109   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     26    5
  16Q GAIN WILD-TYPE  109    4
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               26                109
  1                5                  4
[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 10
  16Q GAIN WILD-TYPE 99 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     24   10
  16Q GAIN WILD-TYPE   99   33
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                24                 99
  YES               10                 33
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   11 27
  16Q GAIN WILD-TYPE 77 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     11   27
  16Q GAIN WILD-TYPE   77   69
                                   clus
vv                                  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   11                 77
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               27                 69
[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      12                         3    20
  16Q GAIN WILD-TYPE    34                         2    94
D29V14, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                   12                 34
  BLACK OR AFRICAN AMERICAN                3                  2
  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"
D29V15, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    1 21
  16Q GAIN WILD-TYPE  5 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   21
  16Q GAIN WILD-TYPE    5   67
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               21                 67
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   20 12
  17P GAIN WILD-TYPE 88 64
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                152 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                 64 
$`17P GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A8NG TCGA-IC-A6RE TCGA-IG-A3QL 
       60.39        18.28         4.31        35.97         7.69        35.21 
TCGA-IG-A50L TCGA-IG-A51D TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4ON 
        0.53        17.03        23.18        25.22         0.30        18.35 
TCGA-L5-A4OQ TCGA-L5-A88Z TCGA-L5-A8NE TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V 
        1.38         7.40        55.50        13.41        13.38        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-R6-A6DN 
       12.49        12.59        12.00        13.18        12.26         8.02 
TCGA-R6-A6KZ TCGA-V5-A7RC TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D 
        5.06         3.42         1.55        18.31        33.70        46.19 
TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.91         2.10 

$`17P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        34.85         8.94        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82         0.36        27.12         5.16        20.02        25.78 
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-A3I8 TCGA-IG-A3Y9 
        8.94        16.24         4.21        32.45        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        47.38        21.70        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25        26.33        32.61        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 
        7.13         7.43        15.48         2.60        25.12         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        12.33        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 
       13.25        12.62        12.46        12.59        12.76        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-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 
       12.33        13.38         0.13        12.03        12.85        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         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-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW 
        8.98        25.81        27.09        22.82        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-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  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 
            12.885             13.035 
[1] "0.3 - 60.4 (12.9)"  "0.1 - 122.1 (13.0)"
[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         9         7
  17P GAIN WILD-TYPE       7        5        6        1        38        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                 9                 38
  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 14  1
  17P GAIN WILD-TYPE    25 36 73  4
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1                7                 25
  T2                   7                 36
  T3                  14                 73
  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   11 16  2  0
  17P GAIN WILD-TYPE 66 52 10  8
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               11                 66
  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    24   1
  17P GAIN WILD-TYPE 111   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     24    1
  17P GAIN WILD-TYPE  111    8
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               24                111
  1                1                  8
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     3  29
  17P GAIN WILD-TYPE  24 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3   29
  17P GAIN WILD-TYPE   24  128
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                3                 24
  MALE                 29                128
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    17  11
  17P GAIN WILD-TYPE 106  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     17   11
  17P GAIN WILD-TYPE  106   32
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                17                106
  YES               11                 32
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   12 20
  17P GAIN WILD-TYPE 76 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     12   20
  17P GAIN WILD-TYPE   76   76
                                   clus
vv                                  17P GAIN MUTATED 17P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   12                 76
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               20                 76
[1] 2 2
[1] FALSE
D30V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    22   2   1   3
  17P GAIN WILD-TYPE 115  10   1   4
D30V12, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               22                115
  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      10                         1    21
  17P GAIN WILD-TYPE    36                         4    93
D30V14, multiclass
                           clus
vv                          17P GAIN MUTATED 17P 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"
D30V15, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0 16
  17P GAIN WILD-TYPE  6 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   16
  17P GAIN WILD-TYPE    6   72
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               16                 72
[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 80 60
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                44                140 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 60 
$`17Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-IG-A3QL 
       60.39        18.28        24.00        35.97        27.12        35.21 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        0.53        17.03        12.82        23.18        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OT 
       30.25         0.30        18.35         3.32         1.38         4.90 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NN TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
        7.40        55.50         5.49        13.38        13.15        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.49        12.76        12.59        12.00        12.33        13.18 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-V5-A7RC 
       12.26         8.02         7.59         5.06        38.40         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D 
       15.35         9.27         1.55        18.31        33.70        46.19 
TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.91         2.10 

$`17Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        34.85         4.31         8.94         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH 
       22.82         0.36         5.16        20.02        25.78        31.27 
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-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OF 
       47.38        21.70        24.03         6.28         3.16        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       32.61        21.01        47.93         7.17         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        12.33        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 
       13.25        12.62        12.46        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-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       25.25        10.52        12.23        12.03        13.18        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
        0.13        12.03        12.85        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW 
        8.98        25.81        27.09        22.82        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-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  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 
            12.985             13.050 
[1] "0.3 - 60.4 (13.0)"  "0.1 - 122.1 (13.1)"
[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        10         7
  17Q GAIN WILD-TYPE       6        5        6        1        37        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                10                 37
  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 21  1
  17Q GAIN WILD-TYPE    25 34 66  4
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1                7                 25
  T2                   9                 34
  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
  17Q GAIN MUTATED   14 18  4  2
  17Q GAIN WILD-TYPE 63 50  8  6
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               14                 63
  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    31   2
  17Q GAIN WILD-TYPE 104   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     31    2
  17Q GAIN WILD-TYPE  104    7
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               31                104
  1                2                  7
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4  40
  17Q GAIN WILD-TYPE  23 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   40
  17Q GAIN WILD-TYPE   23  117
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                4                 23
  MALE                 40                117
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    21  17
  17Q GAIN WILD-TYPE 102  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21   17
  17Q GAIN WILD-TYPE  102   26
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                21                102
  YES               17                 26
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   21 23
  17Q GAIN WILD-TYPE 67 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21   23
  17Q GAIN WILD-TYPE   67   73
                                   clus
vv                                  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   21                 67
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               23                 73
[1] 2 2
[1] FALSE
D31V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    29   4   1   3
  17Q GAIN WILD-TYPE 108   8   1   4
D31V12, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               29                108
  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      13                         2    29
  17Q GAIN WILD-TYPE    33                         3    85
D31V14, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                   13                 33
  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 22
  17Q GAIN WILD-TYPE  6 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   22
  17Q GAIN WILD-TYPE    6   66
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               22                 66
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   27 23
  18P GAIN WILD-TYPE 81 53
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                50                134 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                23                 53 
$`18P GAIN MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A88Y TCGA-L5-A8NT 
       60.39        34.85         4.31         8.94         0.36        27.12 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A97I 
        7.63        13.94         4.21         0.53        12.82        12.16 
TCGA-JY-A6FE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
        3.68        47.93        18.35         1.38         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        7.13         5.49        21.37        13.41        83.24        46.09 
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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.59        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HZ TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC 
       13.18        12.26         5.06        12.69        20.38         3.42 
TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
       16.44        22.82        28.11        18.18        52.27        11.24 
TCGA-XP-A8T6 TCGA-Z6-A8JE 
       25.08         2.10 

$`18P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        18.28        24.00         4.70        19.99        22.82 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       35.97         5.16        20.02        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
       58.55         5.92         8.94        16.24        32.45         7.69 
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-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         3.88         9.30        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
       26.33        32.61        21.01         3.32         7.17        58.59 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NV 
       16.47        13.55        13.22         7.76         8.71        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.41        12.33        13.38        12.46        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HW 
       22.39        12.85        15.52        11.54        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        33.11         7.82         8.02         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-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV 
       15.78         2.89         2.30         7.00         5.29        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       18.31         8.12        33.70        46.19        18.05         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        18.21        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  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 
            12.725             13.300 
[1] "0.4 - 83.2 (12.7)"  "0.1 - 122.1 (13.3)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         1        2        3        0        10        10
  18P GAIN WILD-TYPE       7        3        3        1        37        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           9          4          1          1        3
  18P GAIN WILD-TYPE        16         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                10                 37
  STAGE IIB                10                 21
  STAGE III                 9                 16
  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 13 26  0
  18P GAIN WILD-TYPE    24 30 61  5
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                8                 24
  T2                  13                 30
  T3                  26                 61
  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
  18P GAIN MUTATED   20 22  3  2
  18P GAIN WILD-TYPE 57 46  9  6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               20                 57
  N1               22                 46
  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"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    35   4
  18P GAIN WILD-TYPE 100   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     35    4
  18P GAIN WILD-TYPE  100    5
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               35                100
  1                4                  5
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4  46
  18P GAIN WILD-TYPE  23 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4   46
  18P GAIN WILD-TYPE   23  111
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                 23
  MALE                 46                111
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   29 15
  18P GAIN WILD-TYPE 94 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     29   15
  18P GAIN WILD-TYPE   94   28
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                29                 94
  YES               15                 28
[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  1  3
  18P GAIN WILD-TYPE 98 10  1  4
D32V12, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               39                 98
  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"
D32V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED      16                         2    26
  18P GAIN WILD-TYPE    30                         3    88
D32V14, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                   16                 30
  BLACK OR AFRICAN AMERICAN                2                  3
  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"
D32V15, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2 21
  18P GAIN WILD-TYPE  4 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   21
  18P GAIN WILD-TYPE    4   67
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               21                 67
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   14 10
  18Q GAIN WILD-TYPE 94 66
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                24                160 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                 66 
$`18Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       60.39         0.36         7.63         5.92        13.94         4.21 
TCGA-IG-A3I8 TCGA-IG-A625 TCGA-JY-A6FE TCGA-L5-A43E TCGA-L5-A4OR TCGA-L5-A8NN 
       33.27        12.82         3.68        30.25         3.16         5.49 
TCGA-L5-A8NQ TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FR 
       21.37        12.62        12.76        12.03        13.18        12.26 
TCGA-R6-A6KZ TCGA-S8-A6BW TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-Z6-A8JE 
        5.06        20.38        22.82        52.27        11.24         2.10 

$`18Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN 
       20.02        25.78        31.27        14.30        58.55         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24        32.45         7.69        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
       14.50        12.16       122.10        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         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-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        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-A8HZ TCGA-LN-A8I0 
       25.25        10.52        12.00        12.23        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         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-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        46.19        18.05 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         1.32         2.66        19.73 

  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=" "1.1"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         2        1        1        0         4         2
  18Q GAIN WILD-TYPE       6        4        5        1        43        29
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           8          2          1          0        1
  18Q GAIN WILD-TYPE        17         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                 4                 43
  STAGE IIB                 2                 29
  STAGE III                 8                 17
  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 14  0
  18Q GAIN WILD-TYPE    27 39 73  5
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                5                 27
  T2                   4                 39
  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
  18Q GAIN MUTATED    9 12  1  1
  18Q GAIN WILD-TYPE 68 56 11  7
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                9                 68
  N1               12                 56
  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    19   1
  18Q GAIN WILD-TYPE 116   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     19    1
  18Q GAIN WILD-TYPE  116    8
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               19                116
  1                1                  8
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  22
  18Q GAIN WILD-TYPE  25 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   22
  18Q GAIN WILD-TYPE   25  135
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                 22                135
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    18   4
  18Q GAIN WILD-TYPE 105  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     18    4
  18Q GAIN WILD-TYPE  105   39
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                18                105
  YES                4                 39
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED   11 13
  18Q GAIN WILD-TYPE 77 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     11   13
  18Q GAIN WILD-TYPE   77   83
                                   clus
vv                                  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   11                 77
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               13                 83
[1] 2 2
[1] FALSE
D33V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    20   2   0   1
  18Q GAIN WILD-TYPE 117  10   2   6
D33V12, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               20                117
  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"
D33V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       6                         0    14
  18Q GAIN WILD-TYPE    40                         5   100
D33V14, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    6                 40
  BLACK OR AFRICAN AMERICAN                0                  5
  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"
D33V15, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    0 10
  18Q GAIN WILD-TYPE  6 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   10
  18Q GAIN WILD-TYPE    6   78
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO               10                 78
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   19  9
  19P GAIN WILD-TYPE 89 67
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                28                156 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 9                 67 
$`19P GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-IG-A3QL 
       24.00        35.97        27.12        58.55         8.94        35.21 
TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L7-A56G TCGA-L7-A6VZ 
        3.16         3.32         1.38         3.16        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8I1 
        5.92        13.15        12.59        25.25        12.00        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6XG TCGA-R6-A8WG TCGA-S8-A6BW 
        0.13        12.85        12.26        38.40        12.69        20.38 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EX TCGA-X8-AAAR 
       15.35        27.09        28.11        18.21 

$`19P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36         5.16        20.02 
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-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         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-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93        18.35         7.17 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09        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-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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        33.11         7.82         8.02         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-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.89         2.30         7.00         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        33.70        18.18        52.27        46.19 
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 TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  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 
             13.00              13.05 
[1] "0.1 - 58.5 (13.0)"  "0.3 - 122.1 (13.1)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         1        1        1        0         9         3
  19P GAIN WILD-TYPE       7        4        5        1        38        28
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           2          1          2          2        0
  19P GAIN WILD-TYPE        23         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                 3                 28
  STAGE III                 2                 23
  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  8 12  0
  19P GAIN WILD-TYPE    28 35 75  5
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                4                 28
  T2                   8                 35
  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
  19P GAIN MUTATED   14  5  3  2
  19P GAIN WILD-TYPE 63 63  9  6
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               14                 63
  N1                5                 63
  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    19   8
  19P GAIN WILD-TYPE 104  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     19    8
  19P GAIN WILD-TYPE  104   35
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                19                104
  YES                8                 35
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   13 15
  19P GAIN WILD-TYPE 75 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     13   15
  19P GAIN WILD-TYPE   75   81
                                   clus
vv                                  19P GAIN MUTATED 19P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   13                 75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               15                 81
[1] 2 2
[1] FALSE
D34V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    22   1   0   1
  19P GAIN WILD-TYPE 115  11   2   6
D34V12, multiclass
    clus
vv   19P GAIN MUTATED 19P 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"
D34V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       9                         2    14
  19P GAIN WILD-TYPE    37                         3   100
D34V14, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    9                 37
  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"
D34V15, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1 16
  19P GAIN WILD-TYPE  5 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   16
  19P GAIN WILD-TYPE    5   72
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               16                 72
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   22 18
  19Q GAIN WILD-TYPE 86 58
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                40                144 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                18                 58 
$`19Q GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN 
       24.00        35.97        27.12        58.55         7.63         8.94 
TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A4QS TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH 
       16.24        35.21         3.88         3.16        26.33        32.61 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NV 
        3.32         1.38         3.16        13.55         5.49        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A4A6 
       46.09        10.85        10.36         5.92        15.35        12.85 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6KZ 
       25.25        12.00         0.13        12.85        12.26         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP 
       16.31        38.40        12.69        20.38        15.35        27.09 
TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE 
       28.11        15.91        18.21         2.10 

$`19Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36         5.16        20.02 
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-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27         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-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28        30.25         0.30        21.01        47.93        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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L 
        7.76        21.37         8.71        13.41        83.24        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-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-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        22.39        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-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 
       13.18        12.33        13.38        13.18        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.82         8.02         7.59         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB 
        9.30        15.78         2.89         2.30         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        3.42        16.44         9.27         8.98        25.81        22.82 
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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 
       52.27        46.19        18.05        11.24         9.17        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         3.42         1.32         2.66        19.73 

  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 
             14.45              12.87 
[1] "0.1 - 58.5 (14.4)"  "0.3 - 122.1 (12.9)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         2        1        2        1         9         4
  19Q GAIN WILD-TYPE       6        4        4        0        38        27
                    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                 4                 27
  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  9 18  1
  19Q GAIN WILD-TYPE    26 34 69  4
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                6                 26
  T2                   9                 34
  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 11  4  2
  19Q GAIN WILD-TYPE 60 57  8  6
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               17                 60
  N1               11                 57
  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    24   2
  19Q GAIN WILD-TYPE 111   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     24    2
  19Q GAIN WILD-TYPE  111    7
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               24                111
  1                2                  7
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  39
  19Q GAIN WILD-TYPE  26 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   39
  19Q GAIN WILD-TYPE   26  118
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                 26
  MALE                 39                118
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   32  6
  19Q GAIN WILD-TYPE 91 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     32    6
  19Q GAIN WILD-TYPE   91   37
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                32                 91
  YES                6                 37
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   23 17
  19Q GAIN WILD-TYPE 65 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     23   17
  19Q GAIN WILD-TYPE   65   79
                                   clus
vv                                  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   23                 65
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               17                 79
[1] 2 2
[1] FALSE
D35V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    27   3   1   2
  19Q GAIN WILD-TYPE 110   9   1   5
D35V12, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               27                110
  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       8                         2    25
  19Q GAIN WILD-TYPE    38                         3    89
D35V14, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    8                 38
  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"
D35V15, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1 19
  19Q GAIN WILD-TYPE  5 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   19
  19Q GAIN WILD-TYPE    5   69
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO               19                 69
[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 51 26
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               107                 77 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                50                 26 
$`20P GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.31        24.00         4.70         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       20.02        25.78        31.27         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63        20.12         3.88         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE 
       23.41         4.67        14.50        12.16       122.10         3.68 
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-A43H TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
        0.30        47.93        18.35         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
       29.00         7.13         7.43        15.48         2.60         7.40 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR 
       55.50         2.66        12.92        16.47         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        52.57        46.09        10.85        10.36        10.45 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.33        13.38        13.15        12.62        12.49        12.76 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.85        11.54        12.33        25.25        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.33        13.18         0.13        12.85         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        16.31         7.04         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        2.89        12.69         5.29         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
        8.98        27.09         1.55         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08         2.10         1.32         2.66        19.73 

$`20P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         8.94        19.99 
TCGA-L5-A88T TCGA-Q9-A6FU TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IG-A3YA 
       22.82         5.16        14.30        58.55         7.63        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       18.64         9.30         0.79        12.82         9.96        14.86 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93F TCGA-KH-A6WC 
       44.75        68.02        41.52        47.38        24.03         6.28 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       26.33        32.61        21.01         3.32         7.17         3.16 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
       25.12         3.75         3.02        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
        7.76        21.37        83.24         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-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-RE-A7BO 
       33.11         7.82        38.40        53.95         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
       20.38        15.35        25.81        22.82        12.43        18.31 
TCGA-VR-AA4G TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05        18.21        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 
             12.62              13.48 
[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        1        3        1        24        17
  20P GAIN WILD-TYPE       5        4        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                  1                  4
  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      18 21 52  2
  20P GAIN WILD-TYPE    14 22 35  3
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               18                 14
  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   38 41  7  6
  20P GAIN WILD-TYPE 39 27  5  2
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               38                 39
  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   12 95
  20P GAIN WILD-TYPE 15 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12   95
  20P GAIN WILD-TYPE   15   62
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               12                 15
  MALE                 95                 62
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   74 23
  20P GAIN WILD-TYPE 49 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     74   23
  20P GAIN WILD-TYPE   49   20
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                74                 49
  YES               23                 20
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   57 50
  20P GAIN WILD-TYPE 31 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     57   50
  20P GAIN WILD-TYPE   31   46
                                   clus
vv                                  20P GAIN MUTATED 20P GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   57                 31
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               50                 46
[1] 2 2
[1] FALSE
D36V11, continuous
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   77  8  1  4
  20P GAIN WILD-TYPE 60  4  1  3
D36V12, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               77                 60
  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    69
  20P GAIN WILD-TYPE    24                         2    45
D36V14, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                   22                 24
  BLACK OR AFRICAN AMERICAN                3                  2
  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"
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 48 22
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               114                 70 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                54                 22 
$`20Q GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.31        24.00         4.70         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        31.27        14.30        58.55         7.63 
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-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L 
       33.27         0.85         2.63        20.12         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       17.03        23.41         4.67        14.50        12.16       122.10 
TCGA-JY-A6FE TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
        3.68        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE 
        7.13         7.43        15.48         2.60         7.40        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
        2.66        12.92        16.47        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        13.41        52.57        46.09        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X 
       10.45        12.33        13.38        13.15        12.59        12.62 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX 
       12.49        12.76        12.85        12.33        25.25        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       12.03        13.18        12.33        13.18         0.13        12.85 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30        15.78         2.89        12.69         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        5.29         3.42        16.44         9.27         8.98        27.09 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55         8.12        28.11        18.18        52.27        46.19 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24         9.17        25.08         2.10         2.66        19.73 

$`20Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         8.94        19.99 
TCGA-L5-A88T TCGA-Q9-A6FU TCGA-2H-A9GL TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 
       22.82         5.16         5.92        35.21        20.78        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA 
        9.30         0.79        12.82         9.96        14.86        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OJ 
       68.02        41.52        47.38        24.03         6.28        21.01 
TCGA-L5-A4OP TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NK 
        7.17        25.12         3.75         3.02        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
        7.76        83.24         5.92        12.66        12.43        13.41 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 
       15.35        13.25        12.46        12.59        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       15.52        11.54        12.33        13.22         4.47        10.52 
TCGA-LN-A7HW TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.00        13.38        12.03        12.26        33.11         7.82 
TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EQ 
       53.95         2.30        20.38        15.35        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR 
       12.43        18.31        33.70        18.05        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       41.23        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 
            12.655             13.515 
[1] "0.1 - 122.1 (12.7)" "0.8 - 83.2 (13.5)" 
[1] "hr=" "1.7"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         5        2        3        1        23        19
  20Q GAIN WILD-TYPE       3        3        3        0        24        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED          16          9          6          6        3
  20Q GAIN WILD-TYPE         9          5          3          1        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                  2                  3
  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                6                  1
  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      23 20 55  1
  20Q GAIN WILD-TYPE     9 23 32  4
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               23                  9
  T2                  20                 23
  T3                  55                 32
  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   39 45  7  7
  20Q GAIN WILD-TYPE 38 23  5  1
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               39                 38
  N1               45                 23
  N2                7                  5
  N3                7                  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"
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   78  7
  20Q GAIN WILD-TYPE 57  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     78    7
  20Q GAIN WILD-TYPE   57    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               78                 57
  1                7                  2
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    12 102
  20Q GAIN WILD-TYPE  15  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     12  102
  20Q GAIN WILD-TYPE   15   55
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               12                 15
  MALE                102                 55
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   78 24
  20Q GAIN WILD-TYPE 45 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     78   24
  20Q GAIN WILD-TYPE   45   19
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                78                 45
  YES               24                 19
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   66 48
  20Q GAIN WILD-TYPE 22 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     66   48
  20Q GAIN WILD-TYPE   22   48
                                   clus
vv                                  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   66                 22
  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    73
  20Q GAIN WILD-TYPE    23                         2    41
D37V14, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                   23                 23
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   73                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    4 50
  20Q GAIN WILD-TYPE  2 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4   50
  20Q GAIN WILD-TYPE    2   38
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               50                 38
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   12  4
  21Q GAIN WILD-TYPE 96 72
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                16                168 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 72 
$`21Q GAIN MUTATED`
TCGA-S8-A6BV TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-L5-A4OF 
       20.02         2.63        23.41         4.67        14.50        26.33 
TCGA-L5-A8NE TCGA-L5-A8NN TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 
       55.50         5.49        10.45        15.35        12.59        12.59 
TCGA-LN-A8I1 TCGA-V5-A7RC TCGA-VR-A8EP TCGA-X8-AAAR 
       13.18         3.42        27.09        18.21 

$`21Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       27.12         5.16        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 
        0.79        12.82         9.96        14.86        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        32.61        21.01        47.93        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-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
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-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        13.25        12.62        12.46        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       12.23        12.03        13.18        12.33        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
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-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
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 TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  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 
            13.840             12.885 
[1] "2.6 - 55.5 (13.8)"  "0.1 - 122.1 (12.9)"
[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         3
  21Q GAIN WILD-TYPE       8        5        6        1        41        28
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           1          2          2          0        0
  21Q GAIN WILD-TYPE        24         12          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                 3                 28
  STAGE III                 1                 24
  STAGE IIIA                2                 12
  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  3 10  0
  21Q GAIN WILD-TYPE    30 40 77  5
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                2                 30
  T2                   3                 40
  T3                  10                 77
  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  6  2  0
  21Q GAIN WILD-TYPE 71 62 10  8
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                6                 71
  N1                6                 62
  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    12   0
  21Q GAIN WILD-TYPE 123   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     12    0
  21Q GAIN WILD-TYPE  123    9
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               12                123
  1                0                  9
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2  14
  21Q GAIN WILD-TYPE  25 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2   14
  21Q GAIN WILD-TYPE   25  143
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                2                 25
  MALE                 14                143
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8   6
  21Q GAIN WILD-TYPE 115  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8    6
  21Q GAIN WILD-TYPE  115   37
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 8                115
  YES                6                 37
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    5 11
  21Q GAIN WILD-TYPE 83 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5   11
  21Q GAIN WILD-TYPE   83   85
                                   clus
vv                                  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                    5                 83
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               11                 85
[1] 2 2
[1] FALSE
D38V11, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    11   0   0   0
  21Q GAIN WILD-TYPE 126  12   2   7
D38V12, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               11                126
  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                         1     8
  21Q GAIN WILD-TYPE    39                         4   106
D38V14, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    7                 39
  BLACK OR AFRICAN AMERICAN                1                  4
  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"
D38V15, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    0 12
  21Q GAIN WILD-TYPE  6 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   12
  21Q GAIN WILD-TYPE    6   76
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  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   21 10
  22Q GAIN WILD-TYPE 87 66
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                153 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                 66 
$`22Q GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.31        27.12         5.16        35.21         0.85        20.78 
TCGA-IG-A97H TCGA-L5-A43E TCGA-L5-A4OM TCGA-LN-A49P TCGA-LN-A4A1 TCGA-LN-A4A2 
       14.50        30.25        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-A8HZ TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A8WG 
       12.00        12.23        12.33         0.13        12.85        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       20.38         3.42        27.09         8.12        28.11        18.18 
TCGA-VR-AA7B 
       11.24 

$`22Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36        35.97        20.02 
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-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27         2.63        20.12        18.64         3.88         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-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        21.01        18.35         3.32         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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
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-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
       15.35        12.59        13.25        12.62        12.46        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY 
       22.39        15.52         4.47        25.25        10.52        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18        13.38        13.18        12.03        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         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-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        2.30         7.00         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        22.82        12.43         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        52.27        46.19        18.05         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  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=" "1.2"
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    21   8
  22Q GAIN WILD-TYPE 102  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     21    8
  22Q GAIN WILD-TYPE  102   35
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                21                102
  YES                8                 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 11
  XP GAIN WILD-TYPE 94 65
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               25               159 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               11                65 
$`XP GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88Y TCGA-IG-A51D TCGA-JY-A6F8 TCGA-L5-A4OQ 
        4.31        19.99         0.36        17.03       122.10         1.38 
TCGA-L5-A4OR TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A2 
        3.16         5.49        21.37        13.15        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-R6-A6L4 
       12.59        11.54        13.18        13.18        12.85        16.31 
TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
        2.89         3.42        15.35        33.70        18.18        46.19 
TCGA-ZR-A9CJ 
       19.73 

$`XP GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        22.82        35.97        27.12         5.16        20.02 
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-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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22         7.76         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
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-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       15.35        13.25        12.62        12.46        12.59        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       12.33        13.38         0.13        12.03        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.38         5.29        16.44         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
        8.12        28.11        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        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             12.92 
[1] "0.4 - 122.1 (13.2)" "0.1 - 83.2 (12.9)" 
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         1        1        0        0         9         4
  XP GAIN WILD-TYPE       7        4        6        1        38        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                9                38
  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  5 12  0
  XP GAIN WILD-TYPE    27 38 75  5
D40V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1               5                27
  T2                  5                38
  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   14  4  1  3
  XP GAIN WILD-TYPE 63 64 11  5
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              14                63
  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    15   0
  XP GAIN WILD-TYPE 120   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     15    0
  XP GAIN WILD-TYPE  120    9
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              15               120
  1               0                 9
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     2  23
  XP GAIN WILD-TYPE  25 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2   23
  XP GAIN WILD-TYPE   25  134
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               2                25
  MALE                23               134
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    15   8
  XP GAIN WILD-TYPE 108  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     15    8
  XP GAIN WILD-TYPE  108   35
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               15               108
  YES               8                35
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   10 15
  XP GAIN WILD-TYPE 78 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     10   15
  XP GAIN WILD-TYPE   78   81
                                   clus
vv                                  XP GAIN MUTATED XP GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  10                78
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              15                81
[1] 2 2
[1] FALSE
D40V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    18   0   0   2
  XP GAIN WILD-TYPE 119  12   2   5
D40V12, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              18               119
  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       8                         2    15
  XP GAIN WILD-TYPE    38                         3    99
D40V14, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   8                38
  BLACK OR AFRICAN AMERICAN               2                 3
  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"
D40V15, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    0 14
  XP GAIN WILD-TYPE  6 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   14
  XP GAIN WILD-TYPE    6   74
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              14                74
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   24 17
  XQ GAIN WILD-TYPE 84 59
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               41               143 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               17                59 
$`XQ GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88Y TCGA-S8-A6BV TCGA-2H-A9GI TCGA-IG-A3QL 
        4.31        19.99         0.36        20.02        14.30        35.21 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
        3.88         0.53        17.03        23.41         9.96         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A4OQ TCGA-L5-A8NN TCGA-L5-A8NQ 
      122.10        44.75        23.18         1.38         5.49        21.37 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
        5.92        12.66        12.59        12.62        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.59        11.54        13.18        13.18        12.85        12.26 
TCGA-R6-A6L4 TCGA-R6-A8W8 TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       16.31         2.89        15.35        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       18.18        46.19        14.37         3.42        19.73 

$`XQ GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF 
        4.70        22.82        35.97        27.12         5.16        25.78 
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-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
       20.78         2.63        20.12        18.64         9.30         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE 
       12.82        14.86        14.50        12.16        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.85        10.36        10.45        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 
       13.38        13.15        15.35        13.25        12.46        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.33        13.38         0.13        12.03        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         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-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         3.42        16.44         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX 
       25.81        27.09        22.82        12.43         1.55        28.11 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23         2.10         1.32         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 
            12.85             13.15 
[1] "0.4 - 122.1 (12.8)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         1        0        0        0        13        10
  XQ GAIN WILD-TYPE       7        5        6        1        34        21
                   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               13                34
  STAGE IIB               10                21
  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 10 23  0
  XQ GAIN WILD-TYPE    26 33 64  5
D41V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               6                26
  T2                 10                33
  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
  XQ GAIN MUTATED   19 12  5  3
  XQ GAIN WILD-TYPE 58 56  7  5
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              19                58
  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    31   1
  XQ GAIN WILD-TYPE 104   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     31    1
  XQ GAIN WILD-TYPE  104    8
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              31               104
  1               1                 8
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3  38
  XQ GAIN WILD-TYPE  24 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   38
  XQ GAIN WILD-TYPE   24  119
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               3                24
  MALE                38               119
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   26 11
  XQ GAIN WILD-TYPE 97 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     26   11
  XQ GAIN WILD-TYPE   97   32
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               26                97
  YES              11                32
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   13 28
  XQ GAIN WILD-TYPE 75 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     13   28
  XQ GAIN WILD-TYPE   75   68
                                   clus
vv                                  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  13                75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              28                68
[1] 2 2
[1] FALSE
D41V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    33   0   0   2
  XQ GAIN WILD-TYPE 104  12   2   5
D41V12, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              33               104
  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      17                         2    21
  XQ GAIN WILD-TYPE    29                         3    93
D41V14, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                  17                29
  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"
D41V15, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    1 25
  XQ GAIN WILD-TYPE  5 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   25
  XQ GAIN WILD-TYPE    5   63
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              25                63
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   23 15
  1P LOSS WILD-TYPE 85 61
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               38               146 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15                61 
$`1P LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG TCGA-2H-A9GI 
       60.39         8.94        24.00         4.70        35.97        14.30 
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-JY-A93C 
        7.63        16.24        32.45        33.27        18.64        23.18 
TCGA-L5-A43H TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE 
        0.30         4.90        29.00         2.60         7.40        55.50 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ 
       12.92        16.47        12.33        25.25        12.00        13.18 
TCGA-LN-A8HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 
       12.33         8.02         7.59         5.06         6.35         2.89 
TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER 
        2.30        20.38        16.44         9.27         8.98        12.43 
TCGA-XP-A8T8 TCGA-Z6-A9VB 
       14.37         1.32 

$`1P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         4.31        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH 
        0.36        27.12         5.16        20.02        25.78        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IC-A6RE 
       58.55         5.92        13.94         8.94         4.21         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        20.12         3.88 
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-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38         3.16        58.59         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI 
       15.48        25.12         3.75         3.02         2.66        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       10.52        12.23        12.03        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
       12.03        12.85        12.26        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
        7.04        38.40        53.95         9.30        15.78        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
        7.00         5.29         3.42        15.35        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  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 
            12.38             13.20 
[1] "0.3 - 60.4 (12.4)"  "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         8         4
  1P LOSS WILD-TYPE       6        5        4        1        39        27
                   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                8                39
  STAGE IIB                4                27
  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  8 15  1
  1P LOSS WILD-TYPE    26 35 72  4
D42V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               6                26
  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
  1P LOSS MUTATED   12 15  3  0
  1P LOSS WILD-TYPE 65 53  9  8
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              12                65
  N1              15                53
  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   26  7
  1P LOSS WILD-TYPE 97 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     26    7
  1P LOSS WILD-TYPE   97   36
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               26                97
  YES               7                36
[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   11 11
  1Q LOSS WILD-TYPE 97 65
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               162 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               11                65 
$`1Q LOSS MUTATED`
TCGA-L5-A43M TCGA-L5-A4OE TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A4QS 
        8.94        24.00         7.63        16.24        33.27         3.88 
TCGA-L5-A4OT TCGA-L5-A88V TCGA-LN-A49O TCGA-LN-A5U7 TCGA-LN-A8HZ TCGA-R6-A6DN 
        4.90         2.60        13.41        25.25        12.33         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW 
        7.59         5.06         6.35         2.89         2.30        20.38 
TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8ER TCGA-XP-A8T8 
       16.44         8.98        12.43        14.37 

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

  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 
             8.96             13.20 
[1] "2.3 - 33.3 (9.0)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "2"  
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    13   5
  1Q LOSS WILD-TYPE 110  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     13    5
  1Q LOSS WILD-TYPE  110   38
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               13               110
  YES               5                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    9  1
  2P LOSS WILD-TYPE 99 75
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               174 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                75 
$`2P LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-L5-A4OS TCGA-L5-A8NK TCGA-LN-A7HV TCGA-LN-A7HX 
        2.63        20.12        58.59        13.55        10.52        12.23 
TCGA-R6-A8W8 TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-AAPN 
        2.89        25.81        52.27         2.66 

$`2P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        20.02        25.78        31.27        14.30 
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-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         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-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         1.32        19.73 

  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 
           12.890            13.035 
[1] "2.6 - 58.6 (12.9)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "5.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        0        0         5         1
  2P LOSS WILD-TYPE       8        5        6        1        42        30
                   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                1                30
  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  3  6  0
  2P LOSS WILD-TYPE    32 40 81  5
D44V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               0                32
  T2                  3                40
  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  4  0  0
  2P LOSS WILD-TYPE 72 64 12  8
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               5                72
  N1               4                64
  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     9   0
  2P LOSS WILD-TYPE 126   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    0
  2P LOSS WILD-TYPE  126    9
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               9               126
  1               0                 9
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2   8
  2P LOSS WILD-TYPE  25 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    8
  2P LOSS WILD-TYPE   25  149
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                25
  MALE                 8               149
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     5   4
  2P LOSS WILD-TYPE 118  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    4
  2P LOSS WILD-TYPE  118   39
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                5               118
  YES               4                39
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    2  8
  2P LOSS WILD-TYPE 86 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    8
  2P LOSS WILD-TYPE   86   88
                                   clus
vv                                  2P LOSS MUTATED 2P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   2                86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               8                88
[1] 2 2
[1] FALSE
D44V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     8   1   0   0
  2P LOSS WILD-TYPE 129  11   2   7
D44V12, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               8               129
  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     8
  2P LOSS WILD-TYPE    44                         5   106
D44V14, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   2                44
  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"
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 95 71
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               166 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                71 
$`2Q LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A43H TCGA-L5-A4OS 
        2.63        20.12        18.64         0.79         0.30        58.59 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ 
        3.02        16.47        13.55        10.45        12.46        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-R6-A8W8 TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-AAPN 
       10.52        12.23         2.89        25.81        52.27         2.66 

$`2Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        20.02        25.78        31.27        14.30 
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-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.78         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25        26.33        32.61        21.01        47.93 
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-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         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-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        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-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY 
       13.22         4.47        12.33        25.25        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         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-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        3.42         2.10         1.32        19.73 

  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 112  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11    6
  2Q LOSS WILD-TYPE  112   37
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               11               112
  YES               6                37
[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 42 50
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               92                92 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               26                50 
$`3P LOSS MUTATED`
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A8NG TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GM 
        8.94         4.70        35.97        20.02        14.30        13.94 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12         3.88         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A4OH 
        9.96        14.50        12.16        68.02        30.25        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       21.01         3.32         7.17         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.60         7.40         2.66        12.92        16.47        13.55 
TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       13.41         5.92        12.43        12.33        13.15        15.35 
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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        15.52        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-RE-A7BO 
       12.26        33.11         7.59         7.04         6.35         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW 
       20.38         3.42        25.81        27.09        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        18.05         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

$`3P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF 
       19.99        22.82         0.36        27.12         5.16        25.78 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63         5.92         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP 
       32.45         7.69        18.64         9.30        12.82        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        4.67       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        3.16         0.30        26.33        47.93        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A891 
        3.16        58.59         4.90        29.00        25.12         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02        55.50        13.48        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V 
       10.36        10.45        12.66        13.41        13.38        12.59 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
       13.25        12.59        11.54         7.82         8.02         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-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        2.30        12.69         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA7B 
        8.98        22.82        12.43         1.55        28.11        11.24 
TCGA-XP-A8T8 TCGA-ZR-A9CJ 
       14.37        19.73 

  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 
           12.690            13.445 
[1] "0.1 - 68.0 (12.7)"  "0.3 - 122.1 (13.4)"
[1] "hr=" "1.4"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         4        1        3        1        33        14
  3P LOSS WILD-TYPE       4        4        3        0        14        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED          10         10          3          3        3
  3P LOSS WILD-TYPE        15          4          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               33                14
  STAGE IIB               14                17
  STAGE III               10                15
  STAGE IIIA              10                 4
  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 45  3
  3P LOSS WILD-TYPE    18 17 42  2
D46V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              14                18
  T2                 26                17
  T3                 45                42
  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   48 31  5  3
  3P LOSS WILD-TYPE 29 37  7  5
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              48                29
  N1              31                37
  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   77  4
  3P LOSS WILD-TYPE 58  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     77    4
  3P LOSS WILD-TYPE   58    5
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              77                58
  1               4                 5
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   17 75
  3P LOSS WILD-TYPE 10 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     17   75
  3P LOSS WILD-TYPE   10   82
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              17                10
  MALE                75                82
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   63 22
  3P LOSS WILD-TYPE 60 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     63   22
  3P LOSS WILD-TYPE   60   21
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               63                60
  YES              22                21
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   27 65
  3P LOSS WILD-TYPE 61 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     27   65
  3P LOSS WILD-TYPE   61   31
                                   clus
vv                                  3P LOSS MUTATED 3P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  27                61
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              65                31
[1] 2 2
[1] FALSE
D46V11, continuous
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED   77  2  2  3
  3P LOSS WILD-TYPE 60 10  0  4
D46V12, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              77                60
  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      34                         2    49
  3P LOSS WILD-TYPE    12                         3    65
D46V14, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                  34                12
  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 88 63
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               33               151 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13                63 
$`3Q LOSS MUTATED`
TCGA-JY-A938 TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YA 
       34.85        14.30        13.94         4.21        32.45        20.78 
TCGA-IG-A5S3 TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Z 
       23.41        30.25        32.61         3.32         7.43         7.40 
TCGA-L5-A8NH TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A6 
       12.92         5.92        12.33        15.35        12.46        12.85 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A9FO TCGA-LN-A9FR 
        4.47        12.33        25.25        12.23         0.13        12.26 
TCGA-R6-A6XQ TCGA-RE-A7BO TCGA-VR-A8EP TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-X8-AAAR 
        6.35         7.00        27.09        18.18        46.19        18.21 
TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       25.08         3.42         2.10 

$`3Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
        5.16        20.02        25.78        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        5.92         8.94        16.24         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.13        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
       25.12         3.75         3.02        55.50         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36        10.45        12.66        12.43        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.15        12.59        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        22.39        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       13.22        10.52        12.00        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.38        13.18        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        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-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        22.82        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 
TCGA-ZR-A9CJ 
       19.73 

  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 98 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     25    6
  3Q LOSS WILD-TYPE   98   37
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               25                98
  YES               6                37
[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 45
  4P LOSS WILD-TYPE 48 31
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              105                79 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               45                31 
$`4P LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39         8.94        24.00         4.70        35.97        27.12 
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-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.78        20.12        18.64         3.88         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FH 
       12.82         9.96         4.67        12.16        44.75        47.38 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OT 
       23.18        25.22         3.16        21.01         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NJ 
        7.13         7.43         7.40         3.75        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.55        13.22         8.71        13.41        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U 
        5.92        10.45        12.66        12.43        13.38        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.25        12.62        12.59        12.49        12.76        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        12.85        12.26         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.04         6.35         9.30         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP 
        7.00        20.38         3.42        16.44         9.27        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I 
       18.18        52.27        46.19        18.05        11.24        15.91 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       14.37         3.42         1.32 

$`4P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         4.31        19.99        22.82 
TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE 
        0.36         5.16        20.02        31.27         7.63         7.69 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A97H 
        2.63         9.30        17.03        23.41        14.86        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
      122.10        68.02         3.68        41.52        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NE 
       29.00        15.48         2.60        25.12         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU 
        2.66        13.48         7.76         5.49        21.37        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V 
       52.57        10.85        13.41        12.33        13.15        12.59 
TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HY 
       12.46        12.59        22.39        11.54         4.47        12.03 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 
       12.03        33.11         7.82        16.31        38.40        53.95 
TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EY 
       15.78         5.29        15.35         8.98        25.81        33.70 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        18.21        25.08        41.23         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

  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 
            12.66             15.48 
[1] "0.1 - 60.4 (12.7)"  "0.3 - 122.1 (15.5)"
[1] "hr=" "1.5"
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 27
  4P LOSS WILD-TYPE 55 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     68   27
  4P LOSS WILD-TYPE   55   16
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               68                55
  YES              27                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    3 54
  4P LOSS WILD-TYPE  3 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3   54
  4P LOSS WILD-TYPE    3   34
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              54                34
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   46 42
  4Q LOSS WILD-TYPE 62 34
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               88                96 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               42                34 
$`4Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       60.39         4.31         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       27.12        25.78        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 
        0.85         3.88         0.53         0.79        12.82         4.67 
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OR 
       44.75        47.38        23.18        25.22         3.16         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A891 
        4.90         7.13         7.43        15.48         7.40         3.75 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       12.92        16.47        13.22         8.71        13.41        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       46.09        10.36         5.92        10.45        12.66        13.38 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       15.35        13.25        12.59        12.76        12.85        12.33 
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-A8HZ TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN 
       13.18        12.33         0.13        12.85        12.26         8.02 
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-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
        2.89         2.30        12.69         7.00        20.38        16.44 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EZ 
        9.27        27.09        22.82         1.55        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 
       52.27        11.24        15.91        25.08 

$`4Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        34.85        18.28        19.99        22.82         0.36 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IG-A3YA 
        5.16        20.02        31.27         7.63         7.69        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-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD 
        9.96        14.86        14.50        12.16       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        21.70        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         3.32         7.17         1.38        58.59        29.00 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        2.60        25.12         3.02        55.50         2.66        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L7-A56G 
       13.55         7.76         5.49        21.37        52.57        10.85 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X 
       12.43        13.41        12.33        13.15        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.49        12.59        22.39        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 
       13.22        12.03        13.38        13.18        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-A7RC 
        7.82        16.31        53.95        15.78         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       15.35         8.98        25.81        12.43        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 
       33.70        46.19        18.05         9.17        18.21        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.13              0.30 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            83.24            122.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           12.625            13.960 
[1] "0.1 - 83.2 (12.6)"  "0.3 - 122.1 (14.0)"
[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        19        12
  4Q LOSS WILD-TYPE       5        4        1        0        28        19
                   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               19                28
  STAGE IIB               12                19
  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 22 42  2
  4Q LOSS WILD-TYPE    22 21 45  3
D49V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              10                22
  T2                 22                21
  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   33 33  7  3
  4Q LOSS WILD-TYPE 44 35  5  5
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              33                44
  N1              33                35
  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   63  6
  4Q LOSS WILD-TYPE 72  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     63    6
  4Q LOSS WILD-TYPE   72    3
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              63                72
  1               6                 3
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9 79
  4Q LOSS WILD-TYPE 18 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9   79
  4Q LOSS WILD-TYPE   18   78
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               9                18
  MALE                79                78
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   60 17
  4Q LOSS WILD-TYPE 63 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     60   17
  4Q LOSS WILD-TYPE   63   26
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               60                63
  YES              17                26
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   47 41
  4Q LOSS WILD-TYPE 41 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     47   41
  4Q LOSS WILD-TYPE   41   55
                                   clus
vv                                  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  47                41
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              41                55
[1] 2 2
[1] FALSE
D49V11, continuous
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   62  7  2  3
  4Q LOSS WILD-TYPE 75  5  0  4
D49V12, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              62                75
  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      26                         1    48
  4Q LOSS WILD-TYPE    20                         4    66
D49V14, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                  26                20
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  48                66
[1] 3 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    3 41
  4Q LOSS WILD-TYPE  3 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3   41
  4Q LOSS WILD-TYPE    3   47
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  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 81 57
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               46               138 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               19                57 
$`5P LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GJ 
       60.39        24.00         4.70        27.12        20.02        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A4QS 
        7.63        13.94         8.94         4.21        35.21         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-L5-A43E TCGA-L5-A4OF 
        0.53        17.03         4.67       122.10        30.25        26.33 
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-LN-A49K TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A4A8 
        5.49         8.71         5.92        10.45        12.59        15.52 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-R6-A6XQ 
       10.52        12.03        13.38        33.11        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-AASW TCGA-V5-AASX 
        9.30         2.89         2.30        12.69         9.27         8.98 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-AA4D TCGA-X8-AAAR 
       22.82        12.43        46.19        18.21 

$`5P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        34.85        18.28         4.31         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH 
       22.82         0.36        35.97         5.16        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       14.30         5.92        16.24        32.45         7.69        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-A7DP TCGA-IG-A97H 
        0.79        23.41        12.82         9.96        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.16         0.30        32.61        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NH 
        7.43        15.48        25.12         7.40        55.50        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
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-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        22.39        12.85        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        7.04        53.95        15.78         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET 
        3.42        16.44        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 TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  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             13.20 
[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 90 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     33    8
  5P LOSS WILD-TYPE   90   35
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               33                90
  YES               8                35
[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   52 35
  5Q LOSS WILD-TYPE 56 41
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               87                97 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               35                41 
$`5Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39        24.00         4.70         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
        5.16        20.02        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC 
       16.24         4.21        32.45        35.21         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       18.64         3.88         0.53         4.67        14.50       122.10 
TCGA-JY-A6FH TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
       47.38        31.56        30.25        26.33        21.01        47.93 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V 
        7.17         3.16        58.59         4.90         7.13         2.60 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK 
        3.75         3.02        55.50         2.66        12.92        13.55 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K 
        5.49         8.71        13.41        52.57        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49U TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 
       10.45        12.43        15.35        12.49        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        12.33        10.52        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6XG 
       13.38        13.18        12.85        12.26        33.11        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
        6.35         9.30         2.89         2.30        12.69        20.38 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T6 
        8.12        28.11        52.27        46.19        18.21        25.08 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        2.10         1.32         2.66 

$`5Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        34.85        18.28         4.31         8.94        19.99 
TCGA-L5-A88T TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IC-A6RE 
       22.82        25.78        31.27        14.30         5.92         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       33.27         0.85        20.78         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA 
       23.41        12.82         9.96        14.86        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
       68.02         3.68        41.52        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4ON 
       24.03         6.28         3.16         0.30        32.61        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W 
        3.32         1.38        29.00         7.43        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
        7.40        13.48        16.47        13.22         7.76        21.37 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P 
       83.24        46.09        10.36        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-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       53.95        15.78         7.00         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G 
       15.35         1.55        18.31        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-ZR-A9CJ 
       19.73 

  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 
            12.85             13.22 
[1] "0.4 - 122.1 (12.8)" "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        20        14
  5Q LOSS WILD-TYPE       1        2        5        1        27        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               20                27
  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 20 39  1
  5Q LOSS WILD-TYPE    14 23 48  4
D51V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              18                14
  T2                 20                23
  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   35 35  6  1
  5Q LOSS WILD-TYPE 42 33  6  7
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              35                42
  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   63  5
  5Q LOSS WILD-TYPE 72  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     63    5
  5Q LOSS WILD-TYPE   72    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              63                72
  1               5                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   11 76
  5Q LOSS WILD-TYPE 16 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11   76
  5Q LOSS WILD-TYPE   16   81
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              11                16
  MALE                76                81
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   58 19
  5Q LOSS WILD-TYPE 65 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     58   19
  5Q LOSS WILD-TYPE   65   24
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               58                65
  YES              19                24
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   48 39
  5Q LOSS WILD-TYPE 40 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     48   39
  5Q LOSS WILD-TYPE   40   57
                                   clus
vv                                  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  48                40
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              39                57
[1] 2 2
[1] FALSE
D51V11, continuous
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED   66  6  0  3
  5Q LOSS WILD-TYPE 71  6  2  4
D51V12, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              66                71
  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      21                         2    52
  5Q LOSS WILD-TYPE    25                         3    62
D51V14, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                  21                25
  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 39
  5Q LOSS WILD-TYPE  3 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   39
  5Q LOSS WILD-TYPE    3   49
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              39                49
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   26 12
  6P LOSS WILD-TYPE 82 64
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               146 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12                64 
$`6P LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88Y TCGA-S8-A6BV 
       60.39         4.31         8.94         4.70         0.36        20.02 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A5S3 TCGA-JY-A93C TCGA-L5-A43C 
       33.27        35.21         0.53        23.41        23.18         3.16 
TCGA-L5-A4OR TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K 
        3.16        16.47        13.55        83.24        52.57         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A5U7 
       12.43        13.41        13.25        12.59        12.49        25.25 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC 
       13.18        12.33        13.38         2.30        12.69         3.42 
TCGA-V5-AASW TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-XP-A8T6 TCGA-Z6-A8JD 
        9.27        12.43         8.12        18.18        25.08         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`6P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28        24.00        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       35.97        27.12         5.16        25.78        31.27        14.30 
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-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        32.45         7.69         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        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-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P 
       46.09        10.85        10.36        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-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         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-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       15.78         2.89         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
       15.35         8.98        25.81        27.09        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31        28.11        33.70        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        41.23        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB 
        2.10         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 
           12.640            13.165 
[1] "0.4 - 83.2 (12.6)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
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           3          2          2          2        0
  6P LOSS WILD-TYPE        22         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                3                22
  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 20  1
  6P LOSS WILD-TYPE    28 35 67  4
D52V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               4                28
  T2                  8                35
  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
  6P LOSS MUTATED   21  7  3  2
  6P LOSS WILD-TYPE 56 61  9  6
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              21                56
  N1               7                61
  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    27   0
  6P LOSS WILD-TYPE 108   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     27    0
  6P LOSS WILD-TYPE  108    9
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              27               108
  1               0                 9
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  33
  6P LOSS WILD-TYPE  22 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   33
  6P LOSS WILD-TYPE   22  124
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               5                22
  MALE                33               124
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   25  7
  6P LOSS WILD-TYPE 98 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     25    7
  6P LOSS WILD-TYPE   98   36
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               25                98
  YES               7                36
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   15 23
  6P LOSS WILD-TYPE 73 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     15   23
  6P LOSS WILD-TYPE   73   73
                                   clus
vv                                  6P LOSS MUTATED 6P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  15                73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              23                73
[1] 2 2
[1] FALSE
D52V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    25   3   0   2
  6P LOSS WILD-TYPE 112   9   2   5
D52V12, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              25               112
  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    21
  6P LOSS WILD-TYPE    33                         3    93
D52V14, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                  13                33
  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"
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   24 16
  6Q LOSS WILD-TYPE 84 60
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               40               144 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16                60 
$`6Q LOSS MUTATED`
TCGA-L5-A43M TCGA-L5-A88Y TCGA-S8-A6BV TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94         0.36        20.02        25.78        33.27        35.21 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OR 
        4.67        14.50        47.38        25.22         3.16         3.16 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K 
       16.47        13.55        13.41        83.24        52.57         5.92 
TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR 
       13.41        13.25        12.59        12.49        22.39        13.22 
TCGA-LN-A5U7 TCGA-LN-A8HZ TCGA-R6-A6XG TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
       25.25        12.33        38.40         2.30        12.69        20.38 
TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX 
        3.42         9.27        22.82        12.43         8.12        28.11 
TCGA-VR-A8EZ TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       18.18        25.08         3.42        19.73 

$`6Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
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-A3Y9 
        8.94        16.24         4.21        32.45         7.69         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         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-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85        10.36        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-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         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-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       15.78         2.89         7.00         5.29        16.44        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
        8.98        25.81        27.09         1.55        18.31        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        41.23        14.37         2.10         1.32         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             12.79 
[1] "0.4 - 83.2 (13.5)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0        1        1        0        14         4
  6Q LOSS WILD-TYPE       8        4        5        1        33        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               14                33
  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 21  1
  6Q LOSS WILD-TYPE    29 34 66  4
D53V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               3                29
  T2                  9                34
  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
  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    27   1
  6Q LOSS WILD-TYPE 108   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     27    1
  6Q LOSS WILD-TYPE  108    8
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              27               108
  1               1                 8
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3  37
  6Q LOSS WILD-TYPE  24 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   37
  6Q LOSS WILD-TYPE   24  120
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                37               120
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   25  9
  6Q LOSS WILD-TYPE 98 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     25    9
  6Q LOSS WILD-TYPE   98   34
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               25                98
  YES               9                34
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   18 22
  6Q LOSS WILD-TYPE 70 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18   22
  6Q LOSS WILD-TYPE   70   74
                                   clus
vv                                  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  18                70
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              22                74
[1] 2 2
[1] FALSE
D53V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    27   4   0   1
  6Q LOSS WILD-TYPE 110   8   2   6
D53V12, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              27               110
  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      12                         2    22
  6Q LOSS WILD-TYPE    34                         3    92
D53V14, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                  12                34
  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 20
  6Q LOSS WILD-TYPE  4 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   20
  6Q LOSS WILD-TYPE    4   68
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              20                68
[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 101  70
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               171 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6                70 
$`7P LOSS MUTATED`
TCGA-Q9-A6FU TCGA-2H-A9GI TCGA-IG-A3Y9 TCGA-JY-A6FD TCGA-L5-A4OM TCGA-L5-A4OU 
        5.16        14.30         0.85        68.02        47.93        29.00 
TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NS TCGA-LN-A49L TCGA-LN-A4A8 TCGA-LN-A7HY 
       55.50        13.48        13.41        10.45        15.52        12.03 
TCGA-VR-A8EO 
       25.81 

$`7P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       27.12        20.02        25.78        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27        35.21        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        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-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ 
        7.40         3.75         3.02         2.66        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         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-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        27.09        22.82        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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  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 113  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10    3
  7P LOSS WILD-TYPE  113   40
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               10               113
  YES               3                40
[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   13 10
  7Q LOSS WILD-TYPE 95 66
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               23               161 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10                66 
$`7Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-JY-A6FD 
       25.78        14.30         5.92         0.85         0.79        68.02 
TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NS 
       29.00        55.50        13.48        13.55         8.71        13.41 
TCGA-LN-A49L TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-R6-A6KZ 
       10.45        13.25        12.62        12.03        33.11         5.06 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-AA7I TCGA-Z6-AAPN 
        8.98        25.81         1.55        15.91         2.66 

$`7Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       27.12         5.16        20.02        31.27        58.55         7.63 
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-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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL 
        3.75         3.02         2.66        12.92        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         5.49        21.37        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
       12.33        13.38        13.15        15.35        12.59        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-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-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.23        13.18        12.33 
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-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         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-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
       15.35         9.27        27.09        22.82        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32        19.73 

  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 
            13.25             12.92 
[1] "0.8 - 68.0 (13.2)"  "0.1 - 122.1 (12.9)"
[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           8          1          0          0        0
  7Q LOSS WILD-TYPE        17         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                8                17
  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 16  2
  7Q LOSS WILD-TYPE    32 40 71  3
D55V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               0                32
  T2                  3                40
  T3                 16                71
  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  8  0  0
  7Q LOSS WILD-TYPE 64 60 12  8
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              13                64
  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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    21   0
  7Q LOSS WILD-TYPE 114   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     21    0
  7Q LOSS WILD-TYPE  114    9
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              21               114
  1               0                 9
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3  20
  7Q LOSS WILD-TYPE  24 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3   20
  7Q LOSS WILD-TYPE   24  137
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                20               137
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    16   5
  7Q LOSS WILD-TYPE 107  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     16    5
  7Q LOSS WILD-TYPE  107   38
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               16               107
  YES               5                38
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED   11 12
  7Q LOSS WILD-TYPE 77 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11   12
  7Q LOSS WILD-TYPE   77   84
                                   clus
vv                                  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  11                77
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              12                84
[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       5                         0    13
  7Q LOSS WILD-TYPE    41                         5   101
D55V14, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q 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"
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 22
  8P LOSS WILD-TYPE 68 54
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               62               122 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               22                54 
$`8P LOSS MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A8NT TCGA-Q9-A6FU 
       60.39        34.85         8.94        24.00        27.12         5.16 
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
       25.78         5.92        13.94         7.69         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12         3.88         0.53         0.79        23.41         9.96 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH 
       14.50        44.75        23.18        25.22        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE 
       21.01         3.32         7.43         7.40         3.75        55.50 
TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N 
        2.66         5.49         8.71        10.36        12.66        12.43 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.46        12.59        12.49        22.39        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       12.33        12.00        13.18        12.85        12.26         7.82 
TCGA-R6-A6DN TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-VR-A8ER 
        8.02         2.30        20.38         5.29         3.42        12.43 
TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       18.31        52.27        18.05         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-Z6-AAPN 
       41.23         2.66 

$`8P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        18.28         4.31         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        0.36        35.97        20.02        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
        7.63         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
       35.21        20.78        18.64         9.30        17.03        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         4.67        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        47.38        21.70        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        3.16        30.25         0.30        47.93        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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       15.48         2.60        25.12         3.02        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS 
       16.47        13.55        13.22         7.76        21.37        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.85         5.92        10.45 
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-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       13.25        12.62        12.76        12.59        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       11.54         4.47        25.25        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 
       13.18        12.33        13.38         0.13        12.03        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-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       22.82         1.55         8.12        28.11        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       46.19        11.24        18.21        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        1.32        19.73 

  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 
           12.445            13.380 
[1] "0.5 - 60.4 (12.4)"  "0.1 - 122.1 (13.4)"
[1] "hr=" "1.1"
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          7          5          3        1
  8P LOSS WILD-TYPE        18          7          4          4        4
                   vv
clus                STAGE IVA
  8P LOSS MUTATED           1
  8P LOSS WILD-TYPE         3
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               7                 7
  STAGE IIIB               5                 4
  STAGE IIIC               3                 4
  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
  8P LOSS MUTATED      10 16 30  3
  8P LOSS WILD-TYPE    22 27 57  2
D56V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              10                22
  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 26  7  3
  8P LOSS WILD-TYPE 55 42  5  5
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              22                55
  N1              26                42
  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"
D56V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   51  2
  8P LOSS WILD-TYPE 84  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     51    2
  8P LOSS WILD-TYPE   84    7
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              51                84
  1               2                 7
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     9  53
  8P LOSS WILD-TYPE  18 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      9   53
  8P LOSS WILD-TYPE   18  104
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               9                18
  MALE                53               104
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   44 12
  8P LOSS WILD-TYPE 79 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     44   12
  8P LOSS WILD-TYPE   79   31
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               44                79
  YES              12                31
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   27 35
  8P LOSS WILD-TYPE 61 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     27   35
  8P LOSS WILD-TYPE   61   61
                                   clus
vv                                  8P LOSS MUTATED 8P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  27                61
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              35                61
[1] 2 2
[1] FALSE
D56V11, continuous
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   47  4  1  4
  8P LOSS WILD-TYPE 90  8  1  3
D56V12, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              47                90
  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   14  7
  8Q LOSS WILD-TYPE 94 69
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               163 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7                69 
$`8Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-2H-A9GF TCGA-2H-A9GL TCGA-IG-A5S3 TCGA-JY-A6FA 
       60.39         8.94        25.78         5.92        23.41        44.75 
TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A891 TCGA-L5-A8NE 
       25.22        26.33        32.61        21.01         3.75        55.50 
TCGA-L5-A8NF TCGA-LN-A49N TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HW TCGA-V5-A7RC 
        2.66        12.43        12.33        13.22        12.00         3.42 
TCGA-VR-A8Q7 TCGA-XP-A8T6 TCGA-Z6-AAPN 
       52.27        25.08         2.66 

$`8Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.02        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-A3I8 
        8.94        16.24         4.21        32.45         7.69        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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        3.88         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        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-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
        2.60        25.12         7.40         3.02        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        10.45        12.66        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-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.85        15.52        11.54         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         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-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        41.23        14.37         3.42         2.10         1.32 
TCGA-ZR-A9CJ 
       19.73 

  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 
            21.01             12.85 
[1] "2.7 - 60.4 (21.0)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.7"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         3        0        0        0         3         6
  8Q LOSS WILD-TYPE       5        5        6        1        44        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           3          2          0          0        0
  8Q LOSS WILD-TYPE        22         12          9          7        5
                   vv
clus                STAGE IVA
  8Q LOSS MUTATED           1
  8Q LOSS WILD-TYPE         3
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                3                44
  STAGE IIB                6                25
  STAGE III                3                22
  STAGE IIIA               2                12
  STAGE IIIB               0                 9
  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
  8Q LOSS MUTATED       5  6  9  0
  8Q LOSS WILD-TYPE    27 37 78  5
D57V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               5                27
  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
  8Q LOSS MUTATED    8 11  1  0
  8Q LOSS WILD-TYPE 69 57 11  8
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               8                69
  N1              11                57
  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    17   1
  8Q LOSS WILD-TYPE 118   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     17    1
  8Q LOSS WILD-TYPE  118    8
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              17               118
  1               1                 8
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     3  18
  8Q LOSS WILD-TYPE  24 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3   18
  8Q LOSS WILD-TYPE   24  139
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                24
  MALE                18               139
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    19   1
  8Q LOSS WILD-TYPE 104  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     19    1
  8Q LOSS WILD-TYPE  104   42
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               19               104
  YES               1                42
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED   11 10
  8Q LOSS WILD-TYPE 77 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11   10
  8Q LOSS WILD-TYPE   77   86
                                   clus
vv                                  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  11                77
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              10                86
[1] 2 2
[1] FALSE
D57V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    15   2   0   1
  8Q LOSS WILD-TYPE 122  10   2   6
D57V12, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              15               122
  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       5                         2    11
  8Q LOSS WILD-TYPE    41                         3   103
D57V14, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   5                41
  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  7
  8Q LOSS WILD-TYPE  5 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    7
  8Q LOSS WILD-TYPE    5   81
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO               7                81
[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 46 38
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              100                84 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38                38 
$`9P LOSS MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A8NG TCGA-Q9-A6FU 
       60.39        34.85        18.28         8.94        35.97         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO 
       20.02        25.78        31.27        14.30         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        4.21         7.69        20.78        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
        0.79        23.41         9.96         4.67        14.50        12.16 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       25.22         3.16        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.32         7.17        58.59         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.60         3.75        55.50         2.66        16.47        13.22 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        8.71        13.41        83.24        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-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.03        13.18        12.33         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
       33.11         5.06        16.31        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       15.78         2.30        12.69         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR 
       18.31         8.12        28.11        52.27        46.19        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       41.23        14.37         3.42        19.73 

$`9P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68         4.31        24.00         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
        0.36        27.12        58.55         7.63         5.92        13.94 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45        33.27        35.21         0.85         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.30        17.03        12.82        14.86       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ 
       31.56        24.03         6.28        30.25         0.30        21.01 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A88Z 
        1.38         3.16         4.90        29.00        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02        12.92        13.48        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       21.37        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A9 
       13.41        12.33        13.38        12.59        12.59        11.54 
TCGA-LN-A5U5 TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN 
        4.47        13.38        13.18        12.85         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW 
        7.59         7.04        53.95         2.89         7.00        20.38 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
       15.35        27.09        33.70        18.18        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        9.17        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        26        19
  9P LOSS WILD-TYPE       6        3        3        0        21        12
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED          15          6          4          2        1
  9P LOSS WILD-TYPE        10          8          5          5        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               26                21
  STAGE IIB               19                12
  STAGE III               15                10
  STAGE IIIA               6                 8
  STAGE IIIB               4                 5
  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
  9P LOSS MUTATED      16 27 44  2
  9P LOSS WILD-TYPE    16 16 43  3
D58V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              16                16
  T2                 27                16
  T3                 44                43
  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   39 42  5  2
  9P LOSS WILD-TYPE 38 26  7  6
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              39                38
  N1              42                26
  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"
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 90
  9P LOSS WILD-TYPE 17 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10   90
  9P LOSS WILD-TYPE   17   67
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              10                17
  MALE                90                67
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   62 27
  9P LOSS WILD-TYPE 61 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     62   27
  9P LOSS WILD-TYPE   61   16
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               62                61
  YES              27                16
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   50 50
  9P LOSS WILD-TYPE 38 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     50   50
  9P LOSS WILD-TYPE   38   46
                                   clus
vv                                  9P LOSS MUTATED 9P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  50                38
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              50                46
[1] 2 2
[1] FALSE
D58V11, continuous
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED   77  4  0  2
  9P LOSS WILD-TYPE 60  8  2  5
D58V12, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              77                60
  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      31                         2    54
  9P LOSS WILD-TYPE    15                         3    60
D58V14, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                  31                15
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  54                60
[1] 3 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 52
  9P LOSS WILD-TYPE  1 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      5   52
  9P LOSS WILD-TYPE    1   36
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 1
  NOT HISPANIC OR LATINO              52                36
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   36 29
  9Q LOSS WILD-TYPE 72 47
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               65               119 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29                47 
$`9Q LOSS MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A8NG TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GO 
       18.28         8.94        35.97        25.78        31.27        16.24 
TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 
        4.21         0.85        20.78        18.64         3.88         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A93E TCGA-L5-A4OF 
       23.41         9.96         4.67        14.50        25.22        26.33 
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A8NE 
       47.93        58.59         7.13        15.48         2.60        55.50 
TCGA-L5-A8NF TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        2.66        13.41        83.24        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-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
       13.18         0.13         5.06        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO 
       15.78        12.69         5.29         3.42        16.44        25.81 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        1.55         8.12        28.11        52.27        46.19        11.24 
TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       18.21        14.37         3.42         2.10        19.73 

$`9Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82         0.36        27.12         5.16        20.02 
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-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45         7.69        33.27        35.21         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97I 
        9.30         0.53        17.03        12.82        14.86        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
       30.25         0.30        32.61        21.01        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38         3.16         4.90        29.00         7.43 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.75         3.02        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.62        12.49        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A8I0 TCGA-LN-A9FP 
       12.33        13.22         4.47        25.25        13.38        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       16.31         7.04        53.95         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       20.38        15.35         9.27         8.98        27.09        22.82 
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 
            12.69             13.25 
[1] "0.1 - 83.2 (12.7)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "1.2"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         0        1        3        1        16        14
  9Q LOSS WILD-TYPE       8        4        3        0        31        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           6          6          3          1        1
  9Q LOSS WILD-TYPE        19          8          6          6        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               16                31
  STAGE IIB               14                17
  STAGE III                6                19
  STAGE IIIA               6                 8
  STAGE IIIB               3                 6
  STAGE IIIC               1                 6
  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      10 19 28  2
  9Q LOSS WILD-TYPE    22 24 59  3
D59V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              10                22
  T2                 19                24
  T3                 28                59
  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   26 26  4  2
  9Q LOSS WILD-TYPE 51 42  8  6
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              26                51
  N1              26                42
  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"
D59V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   45  5
  9Q LOSS WILD-TYPE 90  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     45    5
  9Q LOSS WILD-TYPE   90    4
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              45                90
  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 17
  9Q LOSS WILD-TYPE 78 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     45   17
  9Q LOSS WILD-TYPE   78   26
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               45                78
  YES              17                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   48  3  0  2
  9Q LOSS WILD-TYPE 89  9  2  5
D59V12, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              48                89
  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      20                         2    35
  9Q LOSS WILD-TYPE    26                         3    79
D59V14, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                  20                26
  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"
D59V15, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    4 36
  9Q LOSS WILD-TYPE  2 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4   36
  9Q LOSS WILD-TYPE    2   52
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 2
  NOT HISPANIC OR LATINO              36                52
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   31 20
  10P LOSS WILD-TYPE 77 56
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                51                133 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                20                 56 
$`10P LOSS MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-2H-A9GF 
        4.31         8.94        24.00         4.70        27.12        25.78 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 
       14.30         5.92        33.27         0.85         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A4OO 
       23.41        14.50        44.75        23.18         0.30         3.32 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G 
        4.90         7.13        13.55        13.41        83.24        10.85 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.66        13.41        11.54        12.33        13.22         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       25.25        12.00        13.18        12.33        13.38         0.13 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP 
       12.85        12.26         7.82         3.42        16.44        27.09 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-XP-A8T6 
        8.12        28.11        18.18        18.05        11.24        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       14.37         3.42         2.66 

$`10P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        34.85        18.28        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GJ 
        0.36        35.97         5.16        20.02        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
        7.69        35.21        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        3.88         9.30        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16       122.10        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         7.17         1.38         3.16        58.59        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV 
       13.22         7.76         5.49        21.37         8.71        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49P 
       46.09        10.36         5.92        10.45        12.43        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-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       12.85        15.52        12.33        10.52        12.23        12.03 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       13.18        12.03        33.11         8.02         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-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        5.29        15.35         9.27         8.98        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
       12.43         1.55        18.31        33.70        52.27        46.19 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB 
        9.17        15.91        18.21        41.23         2.10         1.32 
TCGA-ZR-A9CJ 
       19.73 

  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              13.18 
[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        10
  10P LOSS WILD-TYPE       7        5        4        1        31        21
                    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                10                 21
  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 15 29  1
  10P LOSS WILD-TYPE    28 28 58  4
D60V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1                4                 28
  T2                  15                 28
  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 14  7  3
  10P LOSS WILD-TYPE 53 54  5  5
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               24                 53
  N1               14                 54
  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   42  4
  10P LOSS WILD-TYPE 93  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     42    4
  10P LOSS WILD-TYPE   93    5
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               42                 93
  1                4                  5
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     8  43
  10P LOSS WILD-TYPE  19 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8   43
  10P LOSS WILD-TYPE   19  114
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                8                 19
  MALE                 43                114
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   35 10
  10P LOSS WILD-TYPE 88 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     35   10
  10P LOSS WILD-TYPE   88   33
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                35                 88
  YES               10                 33
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   15 36
  10P LOSS WILD-TYPE 73 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     15   36
  10P LOSS WILD-TYPE   73   60
                                   clus
vv                                  10P LOSS MUTATED 10P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   15                 73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               36                 60
[1] 2 2
[1] FALSE
D60V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    35   7   1   4
  10P LOSS WILD-TYPE 102   5   1   3
D60V12, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               35                102
  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      19                         4    22
  10P LOSS WILD-TYPE    27                         1    92
D60V14, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                   19                 27
  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 18
  10Q LOSS WILD-TYPE 76 58
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                50                134 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                18                 58 
$`10Q LOSS MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GI 
       24.00         4.70        27.12         5.16        25.78        14.30 
TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 
        5.92        33.27         0.85         2.63         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OO 
       14.50        44.75        23.18         3.16         0.30         3.32 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49M 
        4.90         7.13        13.55        83.24        10.85        12.66 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       13.38        12.46        12.49        22.39        12.85        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY 
       12.33        13.22        12.33        25.25        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-V5-A7RC TCGA-V5-A7RE 
       13.18        13.38        13.18        12.26         3.42        16.44 
TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       27.09        28.11        18.18        25.08        14.37         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

$`10Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV TCGA-2H-A9GH 
       19.99        22.82         0.36        35.97        20.02        31.27 
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-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       32.45         7.69        35.21        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         4.67        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        6.28        30.25        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         7.17         1.38         3.16        58.59        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       52.57        46.09        10.36         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-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       10.52        12.23        12.33         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         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-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55        18.31         8.12        33.70        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        18.21        41.23 
TCGA-Z6-A8JD TCGA-ZR-A9CJ 
        3.42        19.73 

  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 
            12.755             13.185 
[1] "0.3 - 83.2 (12.8)"  "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         8
  10Q LOSS WILD-TYPE       7        5        5        0        31        23
                    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                 8                 23
  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 16 26  1
  10Q LOSS WILD-TYPE    28 27 61  4
D61V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                4                 28
  T2                  16                 27
  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 19  4  2
  10Q LOSS WILD-TYPE 56 49  8  6
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               21                 56
  N1               19                 49
  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   44  2
  10Q LOSS WILD-TYPE 91  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     44    2
  10Q LOSS WILD-TYPE   91    7
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               44                 91
  1                2                  7
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     7  43
  10Q LOSS WILD-TYPE  20 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7   43
  10Q LOSS WILD-TYPE   20  114
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 43                114
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   33 12
  10Q LOSS WILD-TYPE 90 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     33   12
  10Q LOSS WILD-TYPE   90   31
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                33                 90
  YES               12                 31
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   13 37
  10Q LOSS WILD-TYPE 75 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     13   37
  10Q LOSS WILD-TYPE   75   59
                                   clus
vv                                  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   13                 75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               37                 59
[1] 2 2
[1] FALSE
D61V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    36   7   0   3
  10Q LOSS WILD-TYPE 101   5   2   4
D61V12, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               36                101
  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      21                         4    20
  10Q LOSS WILD-TYPE    25                         1    94
D61V14, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                   21                 25
  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 72 60
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                52                132 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                16                 60 
$`11P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A4OG TCGA-L5-A88Y TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL 
       34.85         4.70         0.36        31.27        14.30         5.92 
TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OO 
        4.21         0.85         2.63         3.16         0.30         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE 
        7.17         3.16        15.48         2.60         3.02        55.50 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       16.47        13.55        13.22        10.85        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 
       12.66        12.43        13.41        13.38        13.25        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A8I1 
       12.49        12.76        12.85        12.33        12.03        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8W8 
        0.13        12.85         5.06        38.40         6.35         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8ER 
        2.30        12.69        16.44         9.27        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-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82        35.97        27.12         5.16        20.02 
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-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
       32.45         7.69        33.27        35.21        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        6.28        30.25        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         1.38        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NH 
        7.43        25.12         7.40         3.75         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49S 
       83.24        52.57        46.09         5.92        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
       15.35        12.59        12.62        12.46        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-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO 
       16.31         7.04        53.95         9.30        15.78         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP 
       20.38         5.29         3.42        15.35         8.98        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       22.82         1.55        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.21        41.23         3.42         1.32         2.66        19.73 

  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              14.68 
[1] "0.1 - 55.5 (12.4)"  "0.5 - 122.1 (14.7)"
[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 94 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     29   17
  11P LOSS WILD-TYPE   94   26
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                29                 94
  YES               17                 26
[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   38 22
  11Q LOSS WILD-TYPE 70 54
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                124 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 54 
$`11Q LOSS MUTATED`
TCGA-L5-A4OG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3YC 
        4.70        27.12        20.02         5.92         4.21        20.12 
TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FH TCGA-L5-A43C 
       18.64        23.41         9.96        12.16        47.38         3.16 
TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88S 
        0.30        47.93         3.32         7.17         3.16        15.48 
TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NK TCGA-L5-A8NL 
        2.60         3.02        55.50         2.66        13.55        13.22 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       10.85        10.36        10.45        12.66        12.43        13.38 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       12.59        13.25        12.59        12.49        12.76        12.85 
TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO 
       15.52        12.33        25.25        12.03        13.18         0.13 
TCGA-LN-A9FQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       12.85         5.06         6.35         2.89         2.30        12.69 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ 
        3.42        25.81        12.43        18.31        28.11        18.18 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
        9.17        15.91        25.08        41.23        14.37         2.10 

$`11Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU 
       24.00        19.99        22.82         0.36        35.97         5.16 
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-A3I8 TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        0.85        20.78         2.63         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03         0.79        12.82        14.86         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        68.02         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
       26.33        32.61        21.01        18.35         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.13         7.43        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN 
        3.75        12.92        13.48        16.47         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
        5.92        13.41        12.33        13.15        15.35        12.62 
TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.46        12.59        22.39        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
        4.47        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.38        12.03        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       15.78         7.00        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW 
        9.27         8.98        27.09        22.82         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-X8-AAAR 
       33.70        52.27        46.19        18.05        11.24        18.21 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         1.32         2.66        19.73 

  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 
            12.590             13.445 
[1] "0.1 - 55.5 (12.6)"  "0.4 - 122.1 (13.4)"
[1] "hr=" "1.2"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         2        3        1        1        14        10
  11Q LOSS WILD-TYPE       6        2        5        0        33        21
                    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                10                 21
  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 16 25  2
  11Q LOSS WILD-TYPE    23 27 62  3
D63V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1                9                 23
  T2                  16                 27
  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 23  0  4
  11Q LOSS WILD-TYPE 52 45 12  4
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               25                 52
  N1               23                 45
  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   42  3
  11Q LOSS WILD-TYPE 93  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     42    3
  11Q LOSS WILD-TYPE   93    6
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               42                 93
  1                3                  6
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     8  52
  11Q LOSS WILD-TYPE  19 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8   52
  11Q LOSS WILD-TYPE   19  105
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                8                 19
  MALE                 52                105
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   35 20
  11Q LOSS WILD-TYPE 88 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     35   20
  11Q LOSS WILD-TYPE   88   23
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                35                 88
  YES               20                 23
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   21 39
  11Q LOSS WILD-TYPE 67 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     21   39
  11Q LOSS WILD-TYPE   67   57
                                   clus
vv                                  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   21                 67
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               39                 57
[1] 2 2
[1] FALSE
D63V11, continuous
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED   42  5  1  1
  11Q LOSS WILD-TYPE 95  7  1  6
D63V12, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               42                 95
  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      17                         4    34
  11Q LOSS WILD-TYPE    29                         1    80
D63V14, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                   17                 29
  BLACK OR AFRICAN AMERICAN                4                  1
  WHITE                                   34                 80
[1] 3 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 30
  11Q LOSS WILD-TYPE  2 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4   30
  11Q LOSS WILD-TYPE    2   58
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               30                 58
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   21 13
  12P LOSS WILD-TYPE 87 63
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                34                150 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                13                 63 
$`12P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GM 
       34.85         8.94        20.02        25.78        31.27        13.94 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6FH 
       32.45        33.27         3.88         0.79        14.50        47.38 
TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       25.22        30.25        32.61         7.17         1.38        58.59 
TCGA-L5-A4OW TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NV 
        7.13         3.75         3.02        55.50        12.92        52.57 
TCGA-LN-A49M TCGA-LN-A7HY TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-V5-A7RC 
       12.66        12.03        12.85         7.82         5.06         3.42 
TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       52.27        18.21         2.10        19.73 

$`12P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
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-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21         7.69        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-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       31.56        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT 
       21.01        47.93        18.35         3.32         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        83.24        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        10.45        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-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         8.02         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-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        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 
            14.220             12.835 
[1] "0.8 - 58.6 (14.2)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.4"
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          5          2          1        1
  12P LOSS WILD-TYPE        23          9          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                5                  9
  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 18  0
  12P LOSS WILD-TYPE    24 37 69  5
D64V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                8                 24
  T2                   6                 37
  T3                  18                 69
  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 14  4  1
  12P LOSS WILD-TYPE 65 54  8  7
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               12                 65
  N1               14                 54
  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    25   1
  12P LOSS WILD-TYPE 110   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     25    1
  12P LOSS WILD-TYPE  110    8
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               25                110
  1                1                  8
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     6  28
  12P LOSS WILD-TYPE  21 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6   28
  12P LOSS WILD-TYPE   21  129
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                6                 21
  MALE                 28                129
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   28  2
  12P LOSS WILD-TYPE 95 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     28    2
  12P LOSS WILD-TYPE   95   41
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                28                 95
  YES                2                 41
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   25  9
  12P LOSS WILD-TYPE 63 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     25    9
  12P LOSS WILD-TYPE   63   87
                                   clus
vv                                  12P LOSS MUTATED 12P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   25                 63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                9                 87
[1] 2 2
[1] FALSE
D64V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    25   3   0   3
  12P LOSS WILD-TYPE 112   9   2   4
D64V12, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               25                112
  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    23
  12P LOSS WILD-TYPE    42                         4    91
D64V14, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    4                 42
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   23                 91
[1] 3 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   20 12
  12Q LOSS WILD-TYPE 88 64
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                32                152 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                12                 64 
$`12Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GM TCGA-IG-A3I8 
       34.85         8.94        20.02        31.27        13.94        33.27 
TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A93E 
        3.88         0.79        23.41        14.50        47.38        25.22 
TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A893 
       30.25        32.61         7.17        58.59         7.13         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L7-A56G TCGA-LN-A9FQ TCGA-Q9-A6FW 
       55.50         2.66        12.92        10.85        12.85         7.82 
TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-A8ET TCGA-VR-A8Q7 
        5.06         2.89         3.42         8.98         1.55        52.27 
TCGA-X8-AAAR TCGA-XP-A8T8 
       18.21        14.37 

$`12Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
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-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        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-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       17.03        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        68.02         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       23.18        31.56        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       26.33        21.01        47.93        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16         4.90        29.00         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       25.12         7.40         3.75        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.36         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-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.03        12.26        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         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-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
       20.38         5.29        16.44        15.35         9.27        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        46.19        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 TCGA-ZR-A9CJ 
        2.66        19.73 

  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 
             13.43              13.00 
[1] "0.8 - 58.6 (13.4)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "1.3"
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          3          2          0        1
  12Q LOSS WILD-TYPE        25         11          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                3                 11
  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 12  0
  12Q LOSS WILD-TYPE    22 38 75  5
D65V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               10                 22
  T2                   5                 38
  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
  12Q LOSS MUTATED   12 11  3  0
  12Q LOSS WILD-TYPE 65 57  9  8
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               12                 65
  N1               11                 57
  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    21   2
  12Q LOSS WILD-TYPE 114   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     21    2
  12Q LOSS WILD-TYPE  114    7
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               21                114
  1                2                  7
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     7  25
  12Q LOSS WILD-TYPE  20 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      7   25
  12Q LOSS WILD-TYPE   20  132
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 25                132
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   25  3
  12Q LOSS WILD-TYPE 98 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     25    3
  12Q LOSS WILD-TYPE   98   40
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                25                 98
  YES                3                 40
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   22 10
  12Q LOSS WILD-TYPE 66 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     22   10
  12Q LOSS WILD-TYPE   66   86
                                   clus
vv                                  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   22                 66
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               10                 86
[1] 2 2
[1] FALSE
D65V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    22   1   0   2
  12Q LOSS WILD-TYPE 115  11   2   5
D65V12, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               22                115
  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    23
  12Q LOSS WILD-TYPE    44                         2    91
D65V14, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    2                 44
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   23                 91
[1] 3 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   41 26
  13Q LOSS WILD-TYPE 67 50
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                67                117 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                26                 50 
$`13Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OE TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN 
       60.39        24.00        25.78        58.55         7.63         8.94 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS 
       32.45         7.69        35.21         0.85        20.78         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FD 
        0.53        17.03        23.41         9.96        44.75        68.02 
TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
       25.22        26.33        21.01        47.93         3.16        29.00 
TCGA-L5-A891 TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G 
        3.75        13.22         5.49        13.41        83.24        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36         5.92        10.45        12.43        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.15        15.35        13.25        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX 
       22.39        12.85        13.22        12.33        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FR 
       12.03        12.33        13.38        13.18         0.13        12.26 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-VR-A8EO TCGA-VR-A8EP 
        5.06        38.40         6.35        12.69        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I 
       22.82        18.31        28.11        18.18        52.27        15.91 
TCGA-XP-A8T8 
       14.37 

$`13Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       20.02        31.27        14.30         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        4.21        33.27         2.63        20.12        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
        0.79        12.82        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
      122.10         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       32.61        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV 
       16.47        13.55         7.76        21.37         8.71        52.57 
TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       46.09        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-M9-A5M8 TCGA-Q9-A6FW 
       12.00        13.18        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         7.59        16.31         7.04        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER 
        3.42        16.44        15.35         9.27         8.98        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        1.55         8.12        33.70        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        18.21        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  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 
             13.25              12.62 
[1] "0.1 - 83.2 (13.2)"  "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   41 22
  13Q LOSS WILD-TYPE 82 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     41   22
  13Q LOSS WILD-TYPE   82   21
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                41                 82
  YES               22                 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 85 54
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                139 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                22                 54 
$`14Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39        18.28         8.94        24.00         4.70         0.36 
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
        7.63         8.94        16.24         4.21        32.45        35.21 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FH 
       23.41        12.82         4.67        14.50       122.10        47.38 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OW TCGA-L5-A88S 
       25.22         0.30        26.33        32.61         7.13        15.48 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A56G TCGA-L7-A6VZ 
        3.75        55.50         2.66        16.47        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49W TCGA-LN-A7HV TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ 
       10.45        13.25        10.52        33.11         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-VR-A8EO TCGA-VR-A8EQ 
        6.35         9.30        15.78         7.00        25.81        22.82 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-Z6-AAPN 
       52.27        18.05         2.66 

$`14Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        34.85         4.31        19.99        22.82        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        20.02        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       58.55         5.92        13.94         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I 
        0.53        17.03         0.79         9.96        14.86        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OJ 
       31.56        24.03         6.28         3.16        30.25        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W 
       58.59         4.90        29.00         7.43         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        7.40         3.02        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09         5.92        12.66        12.43        13.41 
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-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-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-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       12.26         7.82         8.02        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         2.89         2.30        12.69        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27         8.98        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-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       18.18        46.19        11.24         9.17        15.91        18.21 
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-ZR-A9CJ 
       19.73 

  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 
             13.25              12.92 
[1] "0.3 - 122.1 (13.2)" "0.1 - 83.2 (12.9)" 
[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 92 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     31    8
  14Q LOSS WILD-TYPE   92   35
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                31                 92
  YES                8                 35
[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 21
  15Q LOSS WILD-TYPE 73 55
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                56                128 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                 55 
$`15Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       34.85        18.28         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
       27.12        20.02         5.92        16.24        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97H 
       35.21        20.12        18.64         3.88         4.67        14.50 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM 
       23.18        31.56        25.22         0.30        32.61        47.93 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        4.90        29.00         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A4A1 
       13.48         5.49         8.71        13.41        83.24        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-R6-A6KZ TCGA-R6-A6XG TCGA-RE-A7BO 
       12.03        12.85        12.26         5.06        38.40         7.00 
TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EU TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JE 
       16.44        25.81        18.31        18.21        14.37         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`15Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
        5.16        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       13.94         8.94         4.21        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82         9.96        14.86        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F 
       68.02         3.68        41.52        47.38        21.70        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON 
        6.28         3.16        30.25        26.33        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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV 
       16.47        13.55        13.22         7.76        21.37        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         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-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        12.85        15.52        11.54        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       10.52        12.00        12.23        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
        0.13        33.11         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        2.30        12.69        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
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-Z6-A8JD TCGA-Z6-A9VB 
        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 
            14.435             12.675 
[1] "0.3 - 83.2 (14.4)"  "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        10
  15Q LOSS WILD-TYPE       5        4        5        1        34        21
                    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                10                 21
  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 11 31  0
  15Q LOSS WILD-TYPE    20 32 56  5
D68V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1               12                 20
  T2                  11                 32
  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 24  5  2
  15Q LOSS WILD-TYPE 55 44  7  6
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               22                 55
  N1               24                 44
  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   42  5
  15Q LOSS WILD-TYPE 93  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     42    5
  15Q LOSS WILD-TYPE   93    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               42                 93
  1                5                  4
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7  49
  15Q LOSS WILD-TYPE  20 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7   49
  15Q LOSS WILD-TYPE   20  108
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 49                108
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   40 12
  15Q LOSS WILD-TYPE 83 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     40   12
  15Q LOSS WILD-TYPE   83   31
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                40                 83
  YES               12                 31
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   34 22
  15Q LOSS WILD-TYPE 54 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     34   22
  15Q LOSS WILD-TYPE   54   74
                                   clus
vv                                  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   34                 54
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               22                 74
[1] 2 2
[1] FALSE
D68V11, continuous
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   42  7  0  3
  15Q LOSS WILD-TYPE 95  5  2  4
D68V12, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               42                 95
  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                         1    37
  15Q LOSS WILD-TYPE    33                         4    77
D68V14, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                   13                 33
  BLACK OR AFRICAN AMERICAN                1                  4
  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    1 26
  15Q LOSS WILD-TYPE  5 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   26
  15Q LOSS WILD-TYPE    5   62
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  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 79 51
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                54                130 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                25                 51 
$`16P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-Q9-A6FU 
       34.85        18.28        24.00         4.70         0.36         5.16 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3YC 
        7.63         5.92        13.94         8.94        32.45        20.12 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OJ 
       47.38        23.18        25.22         3.16        32.61        21.01 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        3.16        58.59         4.90         7.40         3.75         3.02 
TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L 
       12.92         5.49        83.24        52.57        46.09        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A7HW 
       12.43        13.41        12.59        22.39        12.33        12.00 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       12.26         8.02         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.27        27.09        22.82        52.27         2.10         2.66 

$`16P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         4.31         8.94        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       35.97        27.12        20.02        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       58.55        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        18.64         3.88         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-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
       68.02         3.68        41.52        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28        30.25         0.30        26.33        47.93        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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
       15.48         2.60        25.12        55.50         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49P 
       13.41        10.85        10.36         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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.13        12.03        12.85        33.11         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BW 
        5.06        16.31         7.04        38.40        15.78        20.38 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35         8.98        25.81        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       14.37         3.42         1.32        19.73 

  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             13.235 
[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 84 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     39    9
  16P LOSS WILD-TYPE   84   34
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                39                 84
  YES                9                 34
[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 79 52
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                131 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                24                 52 
$`16Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       34.85        18.28         8.94        24.00         4.70         0.36 
TCGA-Q9-A6FU TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
        5.16        31.27         7.63         5.92         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A93C 
       32.45        35.21        20.12        14.50        47.38        23.18 
TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.16        32.61        21.01         3.16        58.59         4.90 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU 
        3.75         3.02        55.50         5.49         8.71        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V 
       46.09        10.85        10.36        10.45        13.41        12.59 
TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       12.33        10.52         5.06         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-A8EP TCGA-VR-A8EQ TCGA-XP-A8T6 TCGA-Z6-AAPN 
        9.27        27.09        22.82        25.08         2.66 

$`16Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        60.39         4.31        19.99        22.82        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM 
       27.12        20.02        25.78        14.30        58.55        13.94 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21         7.69        33.27         0.85        20.78         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       26.33        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49K 
       13.22         7.76        21.37        13.41        52.57         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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RC 
       16.31         7.04        38.40        15.78        20.38         3.42 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35         8.98        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-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        18.21        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32        19.73 

  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 85 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     38   10
  16Q LOSS WILD-TYPE   85   33
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                38                 85
  YES               10                 33
[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   42 30
  17P LOSS WILD-TYPE 66 46
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                72                112 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                30                 46 
$`17P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
       34.85        24.00         4.70         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ 
       20.02        25.78         7.63         5.92         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       32.45        18.64         3.88         0.79        23.41        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
      122.10        47.38        31.56        30.25        26.33        32.61 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        3.32         7.17         4.90         7.13         7.43         2.60 
TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
        3.75        16.47        13.22         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A1 
       83.24         5.92        10.45        13.15        13.25        12.59 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FQ TCGA-M9-A5M8 
       12.33        10.52        13.18        12.33        12.85        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.82         7.59         7.04        38.40         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        2.30        12.69         7.00        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EZ 
        8.98        27.09        22.82        12.43         8.12        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       52.27        11.24        18.21        25.08        14.37         2.66 

$`17P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        18.28         4.31         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM 
       22.82        35.97        31.27        14.30        58.55        13.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
        2.63        20.12         9.30         0.53        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86         4.67        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        21.70        23.18        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28         3.16         0.30        21.01        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88W 
        1.38         3.16        58.59        29.00        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       13.55         7.76        21.37        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.36        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       15.35        12.59        12.62        12.46        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-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        25.25        12.00        12.23        12.03 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-R6-A6DN 
       13.38        13.18         0.13        12.03        12.26         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-S8-A6BW 
        5.06        16.31         6.35        53.95         2.89        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
        5.29         3.42        25.81         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       33.70        46.19        18.05         9.17        15.91        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        3.42         2.10         1.32        19.73 

  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              13.30 
[1] "0.4 - 122.1 (12.6)" "0.1 - 68.0 (13.3)" 
[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        13        14
  17P LOSS WILD-TYPE       4        4        4        1        34        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                13                 34
  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 40  1
  17P LOSS WILD-TYPE    21 31 47  4
D71V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               11                 21
  T2                  12                 31
  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
  17P LOSS MUTATED   25 28  6  4
  17P LOSS WILD-TYPE 52 40  6  4
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               25                 52
  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   53  3
  17P LOSS WILD-TYPE 82  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     53    3
  17P LOSS WILD-TYPE   82    6
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               53                 82
  1                3                  6
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    9 63
  17P LOSS WILD-TYPE 18 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      9   63
  17P LOSS WILD-TYPE   18   94
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                9                 18
  MALE                 63                 94
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   46 16
  17P LOSS WILD-TYPE 77 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     46   16
  17P LOSS WILD-TYPE   77   27
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                46                 77
  YES               16                 27
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   47 25
  17P LOSS WILD-TYPE 41 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     47   25
  17P LOSS WILD-TYPE   41   71
                                   clus
vv                                  17P LOSS MUTATED 17P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   47                 41
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               25                 71
[1] 2 2
[1] FALSE
D71V11, continuous
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   48  6  0  3
  17P LOSS WILD-TYPE 89  6  2  4
D71V12, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               48                 89
  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      12                         3    47
  17P LOSS WILD-TYPE    34                         2    67
D71V14, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                   12                 34
  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 29
  17P LOSS WILD-TYPE  2 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   29
  17P LOSS WILD-TYPE    2   59
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  2
  NOT HISPANIC OR LATINO               29                 59
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   13 13
  17Q LOSS WILD-TYPE 95 63
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                26                158 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                 63 
$`17Q LOSS MUTATED`
TCGA-JY-A938 TCGA-Q9-A6FU TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IC-A6RE 
       34.85         5.16         5.92         8.94         4.21         7.69 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-L5-A4OW TCGA-L5-A891 TCGA-LN-A49L 
        0.79        23.41        14.50         7.13         3.75        10.45 
TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A9FQ TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-V5-A7RE 
       12.59        12.33        12.85         9.30        12.69        16.44 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-X8-AAAR 
        8.98        22.82        12.43        28.11        52.27        18.21 
TCGA-XP-A8T6 TCGA-Z6-AAPN 
       25.08         2.66 

$`17Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       13.94        16.24        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85        10.36         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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30         7.00        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35         9.27        25.81        27.09         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        33.70        18.18        46.19        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-ZR-A9CJ 
        1.32        19.73 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.79               0.13 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             52.27             122.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             12.38              13.22 
[1] "0.8 - 52.3 (12.4)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.6"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0        0        2        0         5         6
  17Q LOSS WILD-TYPE       8        5        4        1        42        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           5          1          1          0        0
  17Q LOSS WILD-TYPE        20         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                 5                 42
  STAGE IIB                 6                 25
  STAGE III                 5                 20
  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       4  4 14  1
  17Q LOSS WILD-TYPE    28 39 73  4
D72V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                4                 28
  T2                   4                 39
  T3                  14                 73
  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 13  1  0
  17Q LOSS WILD-TYPE 69 55 11  8
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                8                 69
  N1               13                 55
  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    21   1
  17Q LOSS WILD-TYPE 114   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21    1
  17Q LOSS WILD-TYPE  114    8
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               21                114
  1                1                  8
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3  23
  17Q LOSS WILD-TYPE  24 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   23
  17Q LOSS WILD-TYPE   24  134
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                3                 24
  MALE                 23                134
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    18   5
  17Q LOSS WILD-TYPE 105  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     18    5
  17Q LOSS WILD-TYPE  105   38
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                18                105
  YES                5                 38
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   13 13
  17Q LOSS WILD-TYPE 75 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     13   13
  17Q LOSS WILD-TYPE   75   83
                                   clus
vv                                  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   13                 75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               13                 83
[1] 2 2
[1] FALSE
D72V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    17   2   0   1
  17Q LOSS WILD-TYPE 120  10   2   6
D72V12, multiclass
    clus
vv   17Q LOSS MUTATED 17Q 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"
D72V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       5                         1    14
  17Q LOSS WILD-TYPE    41                         4   100
D72V14, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    5                 41
  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"
D72V15, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3 13
  17Q LOSS WILD-TYPE  3 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   13
  17Q LOSS WILD-TYPE    3   75
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  3
  NOT HISPANIC OR LATINO               13                 75
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   41 28
  18P LOSS WILD-TYPE 67 48
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                69                115 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                28                 48 
$`18P LOSS MUTATED`
TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
       18.28        24.00         4.70        35.97         5.16        20.02 
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-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       33.27         0.85         2.63         0.79        23.41        14.50 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       47.38        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OX 
       30.25         0.30        26.33        32.61         7.17         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       15.48         2.60         3.75        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A6VZ 
       16.47        13.55        13.22         8.71        52.57        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A4A1 
        5.92        10.45        12.43        13.41        12.33        12.59 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6XG 
       12.03        13.18        12.85         7.82         7.59        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB 
        6.35        53.95         9.30         2.30         7.00         5.29 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW TCGA-X8-AAAR TCGA-XP-A8T7 
        9.27        27.09        18.31         8.12        18.21        41.23 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.66        19.73 

$`18P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85         4.31         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       22.82         0.36        27.12        31.27        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
       13.94         4.21         7.69        35.21        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
       18.64         3.88         9.30         0.53        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A4OJ 
       68.02         3.68        41.52        21.70         6.28        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        4.90        29.00         7.13        25.12         7.40         3.02 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.48         7.76         5.49        21.37        13.41        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       46.09        10.85        12.66        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        13.18        12.33        13.38         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         8.02         5.06        16.31         7.04 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
       15.78         2.89        12.69        20.38         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         8.98        25.81        22.82        12.43         1.55 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       11.24         9.17        15.91        25.08        14.37         2.10 
TCGA-Z6-A9VB 
        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 
             12.92              13.15 
[1] "0.3 - 55.5 (12.9)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "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         8
  18P LOSS WILD-TYPE       5        4        3        1        33        23
                    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                 8                 23
  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  9 40  1
  18P LOSS WILD-TYPE    21 34 47  4
D73V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               11                 21
  T2                   9                 34
  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
  18P LOSS MUTATED   25 26  6  3
  18P LOSS WILD-TYPE 52 42  6  5
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               25                 52
  N1               26                 42
  N2                6                  6
  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   46  4
  18P LOSS WILD-TYPE 89  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     46    4
  18P LOSS WILD-TYPE   89    5
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               46                 89
  1                4                  5
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    12  57
  18P LOSS WILD-TYPE  15 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     12   57
  18P LOSS WILD-TYPE   15  100
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               12                 15
  MALE                 57                100
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   51 10
  18P LOSS WILD-TYPE 72 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     51   10
  18P LOSS WILD-TYPE   72   33
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                51                 72
  YES               10                 33
[1] 2 2
[1] FALSE
D73V9, continuous
D73V10, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   43 26
  18P LOSS WILD-TYPE 45 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     43   26
  18P LOSS WILD-TYPE   45   70
                                   clus
vv                                  18P LOSS MUTATED 18P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   43                 45
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               26                 70
[1] 2 2
[1] FALSE
D73V11, continuous
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   47  8  0  3
  18P LOSS WILD-TYPE 90  4  2  4
D73V12, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               47                 90
  R1                8                  4
  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"
D73V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED      12                         0    49
  18P LOSS WILD-TYPE    34                         5    65
D73V14, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                   12                 34
  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   60 43
  18Q LOSS WILD-TYPE 48 33
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               103                 81 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                43                 33 
$`18Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       34.85        18.28         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        20.02        25.78        31.27        14.30 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
        8.94        16.24        32.45         7.69         0.85         2.63 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
        3.88         0.53         0.79        23.41         9.96        14.50 
TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       12.16        68.02        47.38        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO 
       24.03         3.16         0.30        26.33        32.61         3.32 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       16.47        13.55        13.22         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        10.85        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A5 
       13.41        12.33        13.38        13.25        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
       12.85        12.33        13.22         4.47        12.33        12.23 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.38        13.18        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.59        38.40         6.35        53.95         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EP 
       12.69         7.00         5.29         3.42         9.27        27.09 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       12.43        18.31         8.12        46.19        18.05         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.91        18.21        25.08        41.23         3.42         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`18Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 
       58.55         7.63         5.92        13.94         4.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       35.21        20.78        20.12        18.64         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE 
       12.82        14.86         4.67       122.10        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OM 
       41.52        21.70         6.28        30.25        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88W TCGA-L5-A88Z 
       18.35         1.38         3.16        58.59        25.12         7.40 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-LN-A49K 
       13.48         7.76         5.49        21.37        46.09         5.92 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       13.15        15.35        12.59        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.76        12.59        15.52        11.54        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        12.03        13.18        12.33         0.13        12.03 
TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       12.26         5.06        16.31         7.04         9.30        15.78 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
       20.38        16.44        15.35         8.98        25.81        22.82 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        1.55        28.11        33.70        18.18        52.27        11.24 
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              13.48 
[1] "0.3 - 83.2 (12.8)"  "0.1 - 122.1 (13.5)"
[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          14          7          7          5        4
  18Q LOSS WILD-TYPE        11          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                14                 11
  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  3
  18Q LOSS WILD-TYPE    18 21 35  2
D74V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               14                 18
  T2                  22                 21
  T3                  52                 35
  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
  18Q LOSS MUTATED   38 38  9  5
  18Q LOSS WILD-TYPE 39 30  3  3
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               38                 39
  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   73  6
  18Q LOSS WILD-TYPE 62  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     73    6
  18Q LOSS WILD-TYPE   62    3
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               73                 62
  1                6                  3
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   16 87
  18Q LOSS WILD-TYPE 11 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     16   87
  18Q LOSS WILD-TYPE   11   70
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               16                 11
  MALE                 87                 70
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   68 23
  18Q LOSS WILD-TYPE 55 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     68   23
  18Q LOSS WILD-TYPE   55   20
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                68                 55
  YES               23                 20
[1] 2 2
[1] FALSE
D74V9, continuous
D74V10, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   58 45
  18Q LOSS WILD-TYPE 30 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     58   45
  18Q LOSS WILD-TYPE   30   51
                                   clus
vv                                  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   58                 30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               45                 51
[1] 2 2
[1] FALSE
D74V11, continuous
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED   71  9  2  4
  18Q LOSS WILD-TYPE 66  3  0  3
D74V12, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               71                 66
  R1                9                  3
  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"
D74V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED      23                         3    64
  18Q LOSS WILD-TYPE    23                         2    50
D74V14, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                   23                 23
  BLACK OR AFRICAN AMERICAN                3                  2
  WHITE                                   64                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 27
  19P LOSS WILD-TYPE 71 49
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                64                120 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                27                 49 
$`19P LOSS MUTATED`
TCGA-JY-A938 TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GO 
       34.85        25.78        31.27        14.30         7.63        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        4.21         7.69         2.63         3.88         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH 
       23.41         9.96        14.50       122.10        68.02        47.38 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX 
       30.25        26.33        47.93         7.17        58.59         7.43 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.60         3.75         2.66        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M 
        5.49         8.71        52.57        46.09        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-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 
       12.85         4.47        12.33        12.23        13.18        13.38 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-V5-A7RC TCGA-V5-AASW 
        8.02         5.06         7.04        15.78         3.42         9.27 
TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D 
       25.81         8.12        18.18        52.27        46.19         9.17 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        14.37         2.66        19.73 

$`19P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
        5.16        20.02        58.55         5.92        13.94         8.94 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
       32.45        33.27        35.21         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       18.64         9.30         0.79        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       12.16        44.75         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       32.61        21.01        18.35         3.32         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.13        15.48        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        55.50        12.92        13.48         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       13.41        83.24        10.85        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A3 
       13.41        12.33        13.15        12.59        12.62        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 
       25.25        10.52        12.00        12.03        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        16.31        38.40         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       16.44        15.35         8.98        27.09        22.82        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-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        18.21        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 
            13.200             12.885 
[1] "0.5 - 122.1 (13.2)" "0.1 - 83.2 (12.9)" 
[1] "hr=" "1.1"
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          11          3          2          3        1
  19P LOSS WILD-TYPE        14         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                11                 14
  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      11 13 35  0
  19P LOSS WILD-TYPE    21 30 52  5
D75V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               11                 21
  T2                  13                 30
  T3                  35                 52
  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 31  2  3
  19P LOSS WILD-TYPE 55 37 10  5
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               22                 55
  N1               31                 37
  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  57
  19P LOSS WILD-TYPE  20 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7   57
  19P LOSS WILD-TYPE   20  100
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                7                 20
  MALE                 57                100
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   42 15
  19P LOSS WILD-TYPE 81 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     42   15
  19P LOSS WILD-TYPE   81   28
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                42                 81
  YES               15                 28
[1] 2 2
[1] FALSE
D75V9, continuous
D75V10, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   32 32
  19P LOSS WILD-TYPE 56 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     32   32
  19P LOSS WILD-TYPE   56   64
                                   clus
vv                                  19P LOSS MUTATED 19P LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   32                 56
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               32                 64
[1] 2 2
[1] FALSE
D75V11, continuous
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED   47  3  1  1
  19P LOSS WILD-TYPE 90  9  1  6
D75V12, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               47                 90
  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"
D75V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED      18                         3    35
  19P LOSS WILD-TYPE    28                         2    79
D75V14, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                   18                 28
  BLACK OR AFRICAN AMERICAN                3                  2
  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"
D75V15, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2 29
  19P LOSS WILD-TYPE  4 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   29
  19P LOSS WILD-TYPE    4   59
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               29                 59
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED   33 19
  19Q LOSS WILD-TYPE 75 57
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                52                132 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                19                 57 
$`19Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43J TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GQ 
       34.85         4.31        25.78        31.27        14.30         4.21 
TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
        7.69         2.63         0.53        23.41         9.96        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A4OM TCGA-L5-A4OP 
      122.10        68.02        47.38        30.25        47.93         7.17 
TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NF 
       58.59         7.43        15.48         2.60         3.75         2.66 
TCGA-L5-A8NL TCGA-L5-A8NR TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S 
       13.22         8.71        10.45        12.66        13.38        13.15 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A5U5 TCGA-LN-A5U6 
       13.25        12.46        12.59        12.49         4.47        12.33 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-R6-A6DN TCGA-R6-A8W5 TCGA-R6-A8WC 
       12.23        13.18        13.38         8.02        15.78         2.30 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7D 
        3.42        25.81         8.12        18.18        52.27         9.17 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        14.37         2.66        19.73 

$`19Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       20.02        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE 
       12.82        14.86         4.67        12.16        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16         0.30        26.33        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
        7.13        25.12         7.40         3.02        55.50        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55         7.76         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V 
        5.92        12.43        13.41        12.33        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.62        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       11.54        12.33        13.22        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.03        12.33        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
        7.04        38.40         6.35        53.95         9.30         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       18.31        28.11        33.70        46.19        18.05        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        18.21        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 
            12.905             13.050 
[1] "0.5 - 122.1 (12.9)" "0.1 - 83.2 (13.1)" 
[1] "hr=" "1.2"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         2        2        1        0        13        12
  19Q LOSS WILD-TYPE       6        3        5        1        34        19
                    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                12                 19
  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       8 11 30  0
  19Q LOSS WILD-TYPE    24 32 57  5
D76V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1                8                 24
  T2                  11                 32
  T3                  30                 57
  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   21 23  1  3
  19Q LOSS WILD-TYPE 56 45 11  5
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               21                 56
  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   40  3
  19Q LOSS WILD-TYPE 95  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     40    3
  19Q LOSS WILD-TYPE   95    6
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               40                 95
  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   31 13
  19Q LOSS WILD-TYPE 92 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     31   13
  19Q LOSS WILD-TYPE   92   30
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                31                 92
  YES               13                 30
[1] 2 2
[1] FALSE
D76V9, continuous
D76V10, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   21 31
  19Q LOSS WILD-TYPE 67 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     21   31
  19Q LOSS WILD-TYPE   67   65
                                   clus
vv                                  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   21                 67
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               31                 65
[1] 2 2
[1] FALSE
D76V11, continuous
                    vv
clus                 R0 R1 R2 RX
  19Q LOSS MUTATED   41  1  1  1
  19Q LOSS WILD-TYPE 96 11  1  6
D76V12, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               41                 96
  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      17                         3    26
  19Q LOSS WILD-TYPE    29                         2    88
D76V14, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                   17                 29
  BLACK OR AFRICAN AMERICAN                3                  2
  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"
D76V15, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2 24
  19Q LOSS WILD-TYPE  4 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   24
  19Q LOSS WILD-TYPE    4   64
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  4
  NOT HISPANIC OR LATINO               24                 64
[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 94 71
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                165 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 71 
$`20P LOSS MUTATED`
TCGA-L5-A43M TCGA-2H-A9GI TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A4OF 
        8.94        14.30        44.75        68.02        47.38        26.33 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NL TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O 
       32.61         3.32        13.22        83.24        12.66        13.41 
TCGA-LN-A49Y TCGA-LN-A7HW TCGA-LN-A7HY TCGA-R6-A6XG TCGA-S8-A6BW TCGA-VR-A8EQ 
       12.46        12.00        12.03        38.40        20.38        22.82 
TCGA-XP-A8T8 
       14.37 

$`20P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
        5.16        20.02        25.78        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       14.50        12.16       122.10         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       30.25         0.30        21.01        47.93        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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
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-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-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-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        25.25        10.52        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         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-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  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 
             14.37              12.82 
[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 111  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12    4
  20P LOSS WILD-TYPE  111   39
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                12                111
  YES                4                 39
[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     4   2
  20Q LOSS WILD-TYPE 104  74
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                178 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 74 
$`20Q LOSS MUTATED`
TCGA-L5-A43M TCGA-JY-A6FA TCGA-LN-A7HW TCGA-LN-A9FR TCGA-S8-A6BW TCGA-VR-A8EQ 
        8.94        44.75        12.00        12.26        20.38        22.82 

$`20Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        5.16        20.02        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
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-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-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         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-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              8.94               0.13 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             44.75             122.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            16.320             13.035 
[1] "8.9 - 44.8 (16.3)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "1.4"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0        0        1        0         1         2
  20Q LOSS WILD-TYPE       8        5        5        1        46        29
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           1          0          0          0        0
  20Q LOSS WILD-TYPE        24         14          9          7        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                 2                 29
  STAGE III                 1                 24
  STAGE IIIA                0                 14
  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
  20Q LOSS MUTATED       0  4  2  0
  20Q LOSS WILD-TYPE    32 39 85  5
D78V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                0                 32
  T2                   4                 39
  T3                   2                 85
  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  3  1  0
  20Q LOSS WILD-TYPE 75 65 11  8
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                2                 75
  N1                3                 65
  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"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   0
  20Q LOSS WILD-TYPE 131   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    0
  20Q LOSS WILD-TYPE  131    9
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                4                131
  1                0                  9
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   5
  20Q LOSS WILD-TYPE  26 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    5
  20Q LOSS WILD-TYPE   26  152
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 26
  MALE                  5                152
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   2
  20Q LOSS WILD-TYPE 119  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    2
  20Q LOSS WILD-TYPE  119   41
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 4                119
  YES                2                 41
[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-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-IG-A7DP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HX         TCGA-LN-A7HY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8ET         TCGA-VR-A8EU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4D 
"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    2  4
  20Q LOSS WILD-TYPE 86 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    4
  20Q LOSS WILD-TYPE   86   92
                                   clus
vv                                  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                    2                 86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                4                 92
[1] 2 2
[1] FALSE
D78V11, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     5   0   0   1
  20Q LOSS WILD-TYPE 132  12   2   6
D78V12, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                5                132
  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     2
  20Q LOSS WILD-TYPE    43                         5   112
D78V14, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    3                 43
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    2                112
[1] 3 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   62 46
  21Q LOSS WILD-TYPE 46 30
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               108                 76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                46                 30 
$`21Q LOSS MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       18.28         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       27.12         5.16        25.78         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        8.94        32.45        33.27         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 
       18.64         3.88         0.53         0.79         9.96       122.10 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
        0.30        32.61        21.01        47.93         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
       16.47        13.55        13.22         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.85        10.36         5.92        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.38        13.15        13.25        12.76        12.85        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.22        12.33        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.33        13.38        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASW 
        9.30         2.89         2.30        12.69        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
        8.98        25.81        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        18.18        52.27        46.19        11.24         9.17 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        41.23        14.37         2.10         2.66        19.73 

$`21Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        60.39        34.85        19.99        22.82        35.97 
TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ 
       20.02        31.27        14.30        58.55        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
        7.69        35.21         2.63         9.30        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-KH-A6WC 
       68.02         3.68        41.52        47.38        21.70         6.28 
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88W TCGA-L5-A8NE 
       26.33        18.35         3.32         1.38        25.12        55.50 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L 
       13.48         7.76         5.49        21.37        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       12.66        12.33        15.35        12.59        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.49        12.59        22.39        15.52        11.54 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
        4.47        25.25        10.52        13.18         0.13        12.03 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       16.31        53.95        15.78         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G 
        3.42        15.35        27.09        18.31        33.70        18.05 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        18.21         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 
             12.43              15.35 
[1] "0.3 - 122.1 (12.4)" "0.1 - 83.2 (15.3)" 
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         6        3        5        1        21        15
  21Q LOSS WILD-TYPE       2        2        1        0        26        16
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED          16          8          6          5        3
  21Q LOSS WILD-TYPE         9          6          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                15                 16
  STAGE III                16                  9
  STAGE IIIA                8                  6
  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 21 52  3
  21Q LOSS WILD-TYPE    14 22 35  2
D79V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               18                 14
  T2                  21                 22
  T3                  52                 35
  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 39  7  6
  21Q LOSS WILD-TYPE 35 29  5  2
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               42                 35
  N1               39                 29
  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   77  5
  21Q LOSS WILD-TYPE 58  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     77    5
  21Q LOSS WILD-TYPE   58    4
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               77                 58
  1                5                  4
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   17 91
  21Q LOSS WILD-TYPE 10 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     17   91
  21Q LOSS WILD-TYPE   10   66
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               17                 10
  MALE                 91                 66
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   72 24
  21Q LOSS WILD-TYPE 51 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     72   24
  21Q LOSS WILD-TYPE   51   19
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                72                 51
  YES               24                 19
[1] 2 2
[1] FALSE
D79V9, continuous
D79V10, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   58 50
  21Q LOSS WILD-TYPE 30 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     58   50
  21Q LOSS WILD-TYPE   30   46
                                   clus
vv                                  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   58                 30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               50                 46
[1] 2 2
[1] FALSE
D79V11, continuous
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   76 10  0  6
  21Q LOSS WILD-TYPE 61  2  2  1
D79V12, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               76                 61
  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                         3    70
  21Q LOSS WILD-TYPE    24                         2    44
D79V14, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS 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"
D79V15, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    5 45
  21Q LOSS WILD-TYPE  1 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5   45
  21Q LOSS WILD-TYPE    1   43
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  1
  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 36
  22Q LOSS WILD-TYPE 71 40
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                73                111 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                36                 40 
$`22Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-2H-A9GF 
       34.85        18.28        24.00         4.70         0.36        25.78 
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-A3YB TCGA-IG-A4P3 
        8.94        16.24         4.21        32.45         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6F8 
        3.88         0.53         0.79        23.41         4.67       122.10 
TCGA-JY-A6FH TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OS TCGA-L5-A4OT 
       47.38        31.56         3.16        32.61        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       29.00         7.13         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O 
        8.71        46.09        10.36         5.92        10.45        13.41 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HV 
       13.38        15.35        13.25        12.62        12.76        10.52 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
       12.03        13.18         8.02         7.59         5.06        38.40 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       15.78         2.89         7.00         5.29        16.44         9.27 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN 
       25.81        22.82        18.31        14.37         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`22Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         4.31         8.94        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-IC-A6RE TCGA-IG-A3I8 
       35.97        27.12         5.16        20.02         7.69        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-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96        14.86        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
       68.02         3.68        41.52        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
       24.03         6.28        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NM 
        7.43        15.48         2.60        25.12         3.75         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49M 
       21.37        13.41        83.24        52.57        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.85        12.26        33.11         7.82        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
        6.35        53.95         9.30         2.30        12.69        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        3.42        15.35         8.98        27.09        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        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 
             13.18              12.85 
[1] "0.4 - 122.1 (13.2)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.5"
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          16          4          3          3        3
  22Q LOSS WILD-TYPE         9         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                16                  9
  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 40  0
  22Q LOSS WILD-TYPE    16 33 47  5
D80V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1               16                 16
  T2                  10                 33
  T3                  40                 47
  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 36  3  3
  22Q LOSS WILD-TYPE 53 32  9  5
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               24                 53
  N1               36                 32
  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   54  6
  22Q LOSS WILD-TYPE 81  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     54    6
  22Q LOSS WILD-TYPE   81    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               54                 81
  1                6                  3
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   10 63
  22Q LOSS WILD-TYPE 17 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   63
  22Q LOSS WILD-TYPE   17   94
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               10                 17
  MALE                 63                 94
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   46 19
  22Q LOSS WILD-TYPE 77 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     46   19
  22Q LOSS WILD-TYPE   77   24
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                46                 77
  YES               19                 24
[1] 2 2
[1] FALSE
D80V9, continuous
D80V10, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   49 24
  22Q LOSS WILD-TYPE 39 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     49   24
  22Q LOSS WILD-TYPE   39   72
                                   clus
vv                                  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   49                 39
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               24                 72
[1] 2 2
[1] FALSE
D80V11, continuous
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   55  7  0  2
  22Q LOSS WILD-TYPE 82  5  2  5
D80V12, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               55                 82
  R1                7                  5
  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 71 53
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               60               124 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               23                53 
$`XP LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GI 
       34.85        18.28        24.00        20.02        25.78        14.30 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L 
        4.21        32.45        35.21        20.78         3.88         0.53 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FH 
       23.41        12.82         9.96         4.67        44.75        47.38 
TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 
       23.18        30.25        21.01        18.35         7.17         3.75 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-LN-A49K 
       13.48        16.47         8.71        13.41        46.09         5.92 
TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 
       12.66        12.33        13.38        12.46        12.59        22.39 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A8I0 TCGA-LN-A9FO 
       13.22        25.25        10.52        12.00        13.38         0.13 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A8WC TCGA-R6-A8WG 
       12.26        33.11         8.02         5.06         2.30        12.69 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EW 
       16.44         9.27         8.98        25.81        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       52.27        15.91        25.08        14.37         3.42         2.10 

$`XP LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39         4.31         8.94         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GH 
       22.82         0.36        35.97        27.12         5.16        31.27 
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-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
        7.69        33.27         0.85         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        9.30        17.03         0.79        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
      122.10        68.02         3.68        41.52        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       32.61        47.93         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.02        55.50         2.66        12.92 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.55        13.22         7.76         5.49        21.37        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       52.57        10.85        10.36        10.45        12.43        13.41 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 
       13.15        15.35        12.59        13.25        12.62        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        12.85        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
        4.47        12.33        12.23        12.03        13.18        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 
       13.18        12.03        12.85         7.82         7.59        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-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        2.89         7.00        20.38         5.29         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       27.09        22.82        12.43         1.55        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       18.18        46.19        18.05        11.24         9.17        18.21 
TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23         1.32         2.66        19.73 

  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 
           13.395            12.805 
[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        16        11
  XP LOSS WILD-TYPE       6        4        4        1        31        20
                   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               16                31
  STAGE IIB               11                20
  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   26 22  6  0
  XP LOSS WILD-TYPE 51 46  6  8
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              26                51
  N1              22                46
  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 84 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     39   12
  XP LOSS WILD-TYPE   84   31
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               39                84
  YES              12                31
[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      20                         2    32
  XP LOSS WILD-TYPE    26                         3    82
D81V14, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                  20                26
  BLACK OR AFRICAN AMERICAN               2                 3
  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    3 31
  XP LOSS WILD-TYPE  3 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3   31
  XP LOSS WILD-TYPE    3   57
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              31                57
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   23 16
  XQ LOSS WILD-TYPE 85 60
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39               145 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16                60 
$`XQ LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-2H-A9GR 
       34.85        18.28        24.00        25.78         4.21        32.45 
TCGA-IG-A625 TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP 
       12.82        47.38        30.25        21.01        18.35         7.17 
TCGA-L5-A4OR TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NW 
        3.16         3.75        13.48        16.47         8.71        46.09 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 
       12.33        13.38        12.46        22.39        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A8WC 
       10.52        12.00        33.11         8.02         5.06         2.30 
TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       12.69         3.42        16.44         9.27         8.98        25.81 
TCGA-VR-A8Q7 TCGA-XP-A8T6 TCGA-Z6-A8JE 
       52.27        25.08         2.10 

$`XQ LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39         4.31         8.94         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
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-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79        23.41         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93         3.32         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02        55.50         2.66        12.92        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35        12.59        13.25        12.62 
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-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY 
       11.54        12.33         4.47        12.33        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.85        12.26         7.82         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-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ 
        7.00        20.38         5.29        15.35        27.09        22.82 
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-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        41.23        14.37         3.42         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  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 
            13.38             12.85 
[1] "2.1 - 52.3 (13.4)"  "0.1 - 122.1 (12.8)"
[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        10         4
  XQ LOSS WILD-TYPE       6        3        4        1        37        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               10                37
  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 18  0
  XQ LOSS WILD-TYPE    26 35 69  5
D82V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1               6                26
  T2                  8                35
  T3                 18                69
  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   16 14  2  0
  XQ LOSS WILD-TYPE 61 54 10  8
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              16                61
  N1              14                54
  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    27   0
  XQ LOSS WILD-TYPE 108   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     27    0
  XQ LOSS WILD-TYPE  108    9
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              27               108
  1               0                 9
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3  36
  XQ LOSS WILD-TYPE  24 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   36
  XQ LOSS WILD-TYPE   24  121
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                24
  MALE                36               121
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   24  8
  XQ LOSS WILD-TYPE 99 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     24    8
  XQ LOSS WILD-TYPE   99   35
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               24                99
  YES               8                35
[1] 2 2
[1] FALSE
D82V9, continuous
D82V10, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   25 14
  XQ LOSS WILD-TYPE 63 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     25   14
  XQ LOSS WILD-TYPE   63   82
                                   clus
vv                                  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  25                63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              14                82
[1] 2 2
[1] FALSE
D82V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    27   3   0   2
  XQ LOSS WILD-TYPE 110   9   2   5
D82V12, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              27               110
  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       9                         2    23
  XQ LOSS WILD-TYPE    37                         3    91
D82V14, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   9                37
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                  23                91
[1] 3 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    2 17
  XQ LOSS WILD-TYPE  4 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   17
  XQ LOSS WILD-TYPE    4   71
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 4
  NOT HISPANIC OR LATINO              17                71
[1] 2 2
[1] FALSE
