[1] "ofn"        "-oTPAAD-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/PAAD-TP/15087151/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/15096459/transformed.cor.cli.txt"

nPatients in clinical file=174, in cluster file=184, common to both=173
[1] "Reduce the number of clustering variables from 82 to 79."
[1]  79 173
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               16               157 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               16               157 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               45               128 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               45               128 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13               160 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13               160 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               15               158 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               15               158 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                9               164 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                9               164 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               18               155 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               18               155 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               162 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               162 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               165 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               165 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               27               146 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               27               146 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               153 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               153 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6               167 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6               167 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               169 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               169 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               50               123 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               50               123 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               47               126 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               47               126 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               24               149 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               24               149 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               45               128 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               45               128 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               166 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               166 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               162 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               162 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                165 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                165 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                161 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                161 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                160 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                160 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                158 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                158 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                145 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                145 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                152 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                152 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                26                147 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                26                147 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                25                148 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                25                148 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                13                160 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                13                160 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                151 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                151 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                22                151 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                22                151 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                164 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                164 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                157 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                157 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                26                147 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                26                147 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                161 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                161 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                158 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                158 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                150 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                150 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                34                139 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                34                139 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                130 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                130 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                165 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                165 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               165 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               165 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12               161 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12               161 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               139 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               139 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8               165 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8               165 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               162 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               162 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               168 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               168 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               35               138 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               35               138 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19               154 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19               154 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               150 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               150 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               23               150 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               23               150 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               166 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               166 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10               163 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10               163 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               59               114 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               59               114 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               78                95 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               78                95 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               40               133 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               40               133 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               157 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               157 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               71               102 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               71               102 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               42               131 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               42               131 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                34                139 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                34                139 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                27                146 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                27                146 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                158 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                158 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                14                159 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                14                159 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                18                155 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                18                155 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                24                149 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                24                149 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                153 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                153 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                14                159 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                14                159 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                26                147 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                26                147 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                164 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                164 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                163 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                163 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                74                 99 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                74                 99 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                21                152 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                21                152 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                51                122 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                51                122 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                97                 76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                97                 76 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                156 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                156 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                11                162 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                11                162 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                155 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                155 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                169 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                169 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                53                120 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                53                120 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                43                130 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                43                130 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               25               148 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               25               148 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               17               156 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               17               156 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "NUMBER_PACK_YEARS_SMOKED"              
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[18] "COMPLETENESS_OF_RESECTION"             
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 173 columns.

[1] "Batch" "22"   
[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=88,	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=100,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 173 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "COMPLETENESS_OF_RESECTION"    
[11] "NUMBER_OF_LYMPH_NODES"         "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  8  21 139   4 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  8  21 139   4 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  8  21 139   4 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  8  21 139   4 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=30, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=28, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=16, 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    6  9
  1P GAIN WILD-TYPE 73 83
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               15               156 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9                83 
$`1P GAIN MUTATED`
TCGA-2J-AAB6 TCGA-2J-AABF TCGA-2J-AABP TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-FB-A78T 
        9.63        22.72        11.84         9.60        53.00        12.43 
TCGA-FZ-5923 TCGA-HZ-7925 TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-A6UG TCGA-IB-AAUM 
       20.35        20.19         4.77        19.82         1.35         0.26 
TCGA-M8-A5N4 TCGA-RB-A7B8 TCGA-US-A776 
       19.20        15.32        27.75 

$`1P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABT 
       22.26        31.86        15.91        14.47        14.40        10.49 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        23.61        20.84         7.36        24.26        28.73 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        84.10        68.52        63.85        50.70        30.64 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        31.79        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
       19.27         3.12        17.00         5.88        24.07        14.76 
TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.61        15.95        37.15         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       23.54        15.55         4.04         5.03         1.02         8.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5924 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        15.78        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       12.89        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 
        7.76         0.13         0.26        27.62        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       17.92         4.96        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       49.38        21.90        15.35        23.80        15.65        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        15.12        20.88        21.90         8.22        15.88 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX 
        9.44         8.05        13.28         7.56         9.14        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29         8.78        15.45        13.68         3.12 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        9.40         0.30        21.24        17.26        23.08        22.85 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.26              0.13 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             53.0              84.1 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           15.320            14.155 
[1] "0.3 - 53.0 (15.3)" "0.1 - 84.1 (14.2)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  1P GAIN MUTATED         0        1        0         3        11         0
  1P GAIN WILD-TYPE       1        5       13        23       106         5
                   vv
clus                STAGE IV
  1P GAIN MUTATED          1
  1P GAIN WILD-TYPE        3
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 5
  STAGE IB                0                13
  STAGE IIA               3                23
  STAGE IIB              11               106
  STAGE III               0                 5
  STAGE IV                1                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     1   1  13   1
  1P GAIN WILD-TYPE   7  20 126   3
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               1                 7
  T2               1                20
  T3              13               126
  T4               1                 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"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     4  12
  1P GAIN WILD-TYPE  41 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4   12
  1P GAIN WILD-TYPE   41  112
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               4                41
  1              12               112
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    9  1
  1P GAIN WILD-TYPE 71  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      9    1
  1P GAIN WILD-TYPE   71    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               9                71
  1               1                 3
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    6 10
  1P GAIN WILD-TYPE 72 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6   10
  1P GAIN WILD-TYPE   72   85
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               6                72
  MALE                10                85
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1P GAIN MUTATED                                    13
  1P GAIN WILD-TYPE                                 132
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1P GAIN MUTATED                                       1
  1P GAIN WILD-TYPE                                    21
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  1P GAIN MUTATED                                                  1
  1P GAIN WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  1P GAIN MUTATED                                     1
  1P GAIN WILD-TYPE                                   0
D1V8, multiclass
                                                  clus
vv                                                 1P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 1P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            132
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D1V9, continuous
D1V10, continuous
                   vv
clus                R0 R1 R2 RX
  1P GAIN MUTATED   11  4  0  1
  1P GAIN WILD-TYPE 97 47  2  3
D1V11, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              11                97
  R1               4                47
  R2               0                 2
  RX               1                 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"
D1V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         0    15
  1P GAIN WILD-TYPE     3                         7   143
D1V13, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  15               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  10
  1P GAIN WILD-TYPE   2 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   10
  1P GAIN WILD-TYPE    2  125
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              10               125
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   18 25
  1Q GAIN WILD-TYPE 61 67
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               43               128 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25                67 
$`1Q GAIN MUTATED`
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABP TCGA-2L-AAQJ 
        9.63         2.63        22.72        22.26        11.84        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9IC TCGA-3A-A9IU TCGA-3E-AAAZ TCGA-F2-A44H 
        9.60        53.00        24.26        15.06        71.74        19.27 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ6 TCGA-FZ-5920 
       12.43        15.95        12.53        15.55         8.02         2.01 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-A4BH 
       20.35        15.78        22.06        20.19        17.92         6.38 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7891 
        5.26         0.23         4.77        19.82         4.04        21.30 
TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM 
        3.85        17.16        21.90         1.35         8.22         0.26 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 
       12.46        19.20        15.32        21.24        23.08        27.75 
TCGA-YY-A8LH 
       66.28 

$`1Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABI 
        2.17        23.97        20.61        19.96        22.22        31.86 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV 
       15.91        14.47        14.40        10.49         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        4.70        22.49         3.39        45.47        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        28.73        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        30.64        31.79        34.09        10.13        12.39 
TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       75.12        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A7DR 
        3.12        17.00         5.88        24.07        14.76        11.61 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        34.82        23.54         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5926 TCGA-H6-8124 
        1.02        24.36         5.10        36.20        17.79        12.89 
TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       13.84        21.73         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.26        27.62        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
       16.14        10.13        21.60        10.85         1.08        12.95 
TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       49.38        21.90        15.35        23.80        15.65        41.33 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7897 TCGA-IB-8126 
        3.62        43.79        15.81        19.66        15.98         2.47 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 
       12.00        15.85         7.20        15.12        20.88        15.88 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX 
        9.44         8.05        13.28         7.56         9.14        12.92 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M 
       10.29         8.78        15.45        13.68         3.12         9.40 
TCGA-RL-AAAS TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
        0.30        17.26        22.85        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76         0.69 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.23              0.13 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            71.74             84.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           15.550            13.825 
[1] "0.2 - 71.7 (15.6)" "0.1 - 84.1 (13.8)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  1Q GAIN MUTATED         0        2        1        11        28         1
  1Q GAIN WILD-TYPE       1        4       12        15        89         4
                   vv
clus                STAGE IV
  1Q GAIN MUTATED          2
  1Q GAIN WILD-TYPE        2
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                2                 4
  STAGE IB                1                12
  STAGE IIA              11                15
  STAGE IIB              28                89
  STAGE III               1                 4
  STAGE IV                2                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q GAIN MUTATED     2   3  38   2
  1Q GAIN WILD-TYPE   6  18 101   2
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               2                 6
  T2               3                18
  T3              38               101
  T4               2                 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"
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   16 29
  1Q GAIN WILD-TYPE 29 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     16   29
  1Q GAIN WILD-TYPE   29   95
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              16                29
  1              29                95
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   19  2
  1Q GAIN WILD-TYPE 61  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     19    2
  1Q GAIN WILD-TYPE   61    2
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              19                61
  1               2                 2
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   15 30
  1Q GAIN WILD-TYPE 63 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     15   30
  1Q GAIN WILD-TYPE   63   65
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              15                63
  MALE                30                65
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1Q GAIN MUTATED                                    40
  1Q GAIN WILD-TYPE                                 105
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1Q GAIN MUTATED                                       3
  1Q GAIN WILD-TYPE                                    19
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  1Q GAIN MUTATED                                                  1
  1Q GAIN WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  1Q GAIN MUTATED                                     1
  1Q GAIN WILD-TYPE                                   0
D2V8, multiclass
                                                  clus
vv                                                 1Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           40
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 1Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            105
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D2V9, continuous
D2V10, continuous
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   31 12  0  1
  1Q GAIN WILD-TYPE 77 39  2  3
D2V11, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              31                77
  R1              12                39
  R2               0                 2
  RX               1                 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"
D2V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         2    41
  1Q GAIN WILD-TYPE     2                         5   117
D2V13, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  41               117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2  33
  1Q GAIN WILD-TYPE   1 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   33
  1Q GAIN WILD-TYPE    1  102
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              33               102
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    8  5
  2P GAIN WILD-TYPE 71 87
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13               158 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                5                87 
$`2P GAIN MUTATED`
TCGA-2J-AABO TCGA-2L-AAQL TCGA-3A-A9J0 TCGA-FB-A545 TCGA-FB-AAPZ TCGA-IB-7651 
       14.47         9.60        12.39        24.07        23.54        19.82 
TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-AAUU TCGA-YB-A89D 
        4.04         3.85        17.16        15.85         8.05        11.51 
TCGA-YH-A8SY 
       12.76 

$`2P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABP 
       22.22        22.72        22.26        31.86        15.91        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95        45.47        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        28.73        60.95        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       10.13        75.12        71.74        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
        7.10         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       14.76        12.43        11.61        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        34.82        15.55         4.04         5.03         1.02 
TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        8.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
       15.78        17.79        12.89        13.84        22.06        21.73 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
        0.92        19.50         7.76         0.13         0.26        27.62 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       20.19        17.03        23.21        12.03         0.69         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 
       15.35        23.80        15.65        41.33         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
       15.81        19.66        21.30        15.98         2.47        12.00 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
       11.11         7.40         9.44        13.28         7.56         9.14 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       13.68         3.12        15.32         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             3.85              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            24.07             84.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           12.760            14.285 
[1] "3.9 - 24.1 (12.8)" "0.1 - 84.1 (14.3)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  2P GAIN MUTATED         0        0        0         2        10         1
  2P GAIN WILD-TYPE       1        6       13        24       107         4
                   vv
clus                STAGE IV
  2P GAIN MUTATED          0
  2P GAIN WILD-TYPE        4
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                0                13
  STAGE IIA               2                24
  STAGE IIB              10               107
  STAGE III               1                 4
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED     0   1  12   0
  2P GAIN WILD-TYPE   8  20 127   4
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               0                 8
  T2               1                20
  T3              12               127
  T4               0                 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"
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  11
  2P GAIN WILD-TYPE  43 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   11
  2P GAIN WILD-TYPE   43  113
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               2                43
  1              11               113
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    8  0
  2P GAIN WILD-TYPE 72  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8    0
  2P GAIN WILD-TYPE   72    4
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               8                72
  1               0                 4
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3 10
  2P GAIN WILD-TYPE 75 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   10
  2P GAIN WILD-TYPE   75   85
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                75
  MALE                10                85
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2P GAIN MUTATED                                    12
  2P GAIN WILD-TYPE                                 133
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2P GAIN MUTATED                                       0
  2P GAIN WILD-TYPE                                    22
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  2P GAIN MUTATED                                                  0
  2P GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  2P GAIN MUTATED                                     0
  2P GAIN WILD-TYPE                                   1
D3V8, multiclass
                                                  clus
vv                                                 2P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 2P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            133
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           22
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D3V9, continuous
D3V10, continuous
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED     7   3   0   1
  2P GAIN WILD-TYPE 101  48   2   3
D3V11, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               7               101
  R1               3                48
  R2               0                 2
  RX               1                 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"
D3V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0    13
  2P GAIN WILD-TYPE     3                         7   145
D3V13, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  13               145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  10
  2P GAIN WILD-TYPE   3 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   10
  2P GAIN WILD-TYPE    3  125
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              10               125
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   10  5
  2Q GAIN WILD-TYPE 69 87
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               15               156 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5                87 
$`2Q GAIN MUTATED`
TCGA-2J-AABE TCGA-2J-AABO TCGA-2L-AAQL TCGA-3A-A9J0 TCGA-FB-A545 TCGA-FB-AAPZ 
       22.22        14.47         9.60        12.39        24.07        23.54 
TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP 
       10.85        19.82         4.04         3.85        17.16        15.85 
TCGA-IB-AAUU TCGA-YB-A89D TCGA-YH-A8SY 
        8.05        11.51        12.76 

$`2Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR 
       22.72        22.26        31.86        15.91        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95        45.47        53.00        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        28.73        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        30.64        15.06        31.79        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM 
        7.66        19.27         3.12        17.00         5.88        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       12.43        11.61        15.95        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       34.82        15.55         4.04         5.03         1.02         8.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 
       24.36         2.01         5.10        36.20        20.35        15.78 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
       17.79        12.89        13.84        22.06        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
       19.50         7.76         0.13         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
       12.43        14.93        17.92         4.96        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A8P1 
       10.13         6.38        21.60         5.26         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       12.95        49.38         4.77        21.90        15.35        23.80 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       15.65        41.33         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS 
       21.30        15.98         2.47        12.00         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        9.44        13.28         7.56         9.14        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        27.75        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.81        12.99        12.03        13.32        66.28         0.69 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             3.85              0.13 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            24.07             84.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           12.760            14.285 
[1] "3.9 - 24.1 (12.8)" "0.1 - 84.1 (14.3)"
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  2Q GAIN MUTATED         0        0        0         3        11         1
  2Q GAIN WILD-TYPE       1        6       13        23       106         4
                   vv
clus                STAGE IV
  2Q GAIN MUTATED          0
  2Q GAIN WILD-TYPE        4
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                0                13
  STAGE IIA               3                23
  STAGE IIB              11               106
  STAGE III               1                 4
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED     0   1  14   0
  2Q GAIN WILD-TYPE   8  20 125   4
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               0                 8
  T2               1                20
  T3              14               125
  T4               0                 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"
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     3  12
  2Q GAIN WILD-TYPE  42 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   12
  2Q GAIN WILD-TYPE   42  112
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               3                42
  1              12               112
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    9  0
  2Q GAIN WILD-TYPE 71  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9    0
  2Q GAIN WILD-TYPE   71    4
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               9                71
  1               0                 4
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3 12
  2Q GAIN WILD-TYPE 75 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   12
  2Q GAIN WILD-TYPE   75   83
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               3                75
  MALE                12                83
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2Q GAIN MUTATED                                    13
  2Q GAIN WILD-TYPE                                 132
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2Q GAIN MUTATED                                       1
  2Q GAIN WILD-TYPE                                    21
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  2Q GAIN MUTATED                                                  0
  2Q GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  2Q GAIN MUTATED                                     0
  2Q GAIN WILD-TYPE                                   1
D4V8, multiclass
                                                  clus
vv                                                 2Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 2Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            132
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D4V9, continuous
D4V10, continuous
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED    9  3  0  1
  2Q GAIN WILD-TYPE 99 48  2  3
D4V11, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               9                99
  R1               3                48
  R2               0                 2
  RX               1                 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"
D4V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0    15
  2Q GAIN WILD-TYPE     3                         7   143
D4V13, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  15               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  11
  2Q GAIN WILD-TYPE   3 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   11
  2Q GAIN WILD-TYPE    3  124
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              11               124
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    4  5
  3P GAIN WILD-TYPE 75 87
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                9               162 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                87 
$`3P GAIN MUTATED`
TCGA-2J-AAB6 TCGA-3A-A9J0 TCGA-FB-A5VM TCGA-FB-AAPZ TCGA-HZ-7922 TCGA-IB-7646 
        9.63        12.39        14.76        23.54         0.13         4.77 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-A6UG 
       19.66         3.85         1.35 

$`3P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.72        22.26        31.86        15.91        14.47        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
        3.39        12.95         9.60        45.47        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        30.64        15.06        31.79 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       34.09        10.13        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ 
        5.88        24.07        12.43        11.61        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        34.82        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       20.35        15.78        17.79        12.89        13.84        22.06 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 
       21.73         0.92        19.50         7.76         0.26        27.62 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       20.19        17.03        23.21        12.03         0.69         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 
        1.08         0.23        12.95        49.38        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       19.82        23.80        15.65        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       43.79        15.81        21.30        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
        6.02        11.11         7.40         9.44         8.05        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.56         9.14        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.13              0.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            23.54             84.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            9.630            14.435 
[1] "0.1 - 23.5 (9.6)"  "0.2 - 84.1 (14.4)"
[1] "hr=" "1.8"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  3P GAIN MUTATED         0        0        2         2         5         0
  3P GAIN WILD-TYPE       1        6       11        24       112         5
                   vv
clus                STAGE IV
  3P GAIN MUTATED          0
  3P GAIN WILD-TYPE        4
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                2                11
  STAGE IIA               2                24
  STAGE IIB               5               112
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED     0   3   6   0
  3P GAIN WILD-TYPE   8  18 133   4
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               0                 8
  T2               3                18
  T3               6               133
  T4               0                 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"
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4   5
  3P GAIN WILD-TYPE  41 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4    5
  3P GAIN WILD-TYPE   41  119
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               4                41
  1               5               119
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    6  0
  3P GAIN WILD-TYPE 74  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    0
  3P GAIN WILD-TYPE   74    4
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               6                74
  1               0                 4
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  8
  3P GAIN WILD-TYPE 77 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    8
  3P GAIN WILD-TYPE   77   87
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                77
  MALE                 8                87
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3P GAIN MUTATED                                     9
  3P GAIN WILD-TYPE                                 136
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3P GAIN MUTATED                                       0
  3P GAIN WILD-TYPE                                    22
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  3P GAIN MUTATED                                                  0
  3P GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  3P GAIN MUTATED                                     0
  3P GAIN WILD-TYPE                                   1
D5V8, multiclass
                                                  clus
vv                                                 3P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 3P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            136
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           22
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D5V9, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                52 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-2J-AABI        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-6880        TCGA-F2-A8YN        TCGA-FB-A4P5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-7886 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-IB-AAUV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL        TCGA-YY-A8LH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V10, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                43 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A78T        TCGA-FB-A7DR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUV        TCGA-LB-A7SX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-US-A774 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YY-A8LH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED     7   2   0   0
  3P GAIN WILD-TYPE 101  49   2   4
D5V11, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               7               101
  R1               2                49
  R2               0                 2
  RX               0                 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"
D5V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0     8
  3P GAIN WILD-TYPE     3                         7   150
D5V13, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   8               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0   7
  3P GAIN WILD-TYPE   3 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    7
  3P GAIN WILD-TYPE    3  128
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               7               128
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    4 14
  3Q GAIN WILD-TYPE 75 78
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               18               153 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               14                78 
$`3Q GAIN MUTATED`
TCGA-2J-AAB6 TCGA-2L-AAQL TCGA-3A-A9IB TCGA-3A-A9J0 TCGA-FB-A5VM TCGA-FB-AAPZ 
        9.63         9.60         7.36        12.39        14.76        23.54 
TCGA-FB-AAQ1 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-IB-7646 TCGA-IB-7647 
        4.04         0.13         3.95        17.92         4.77        21.90 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUO TCGA-RB-A7B8 
       19.66         3.85         1.35         8.22         7.86        15.32 

$`3Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.72        22.26        31.86        15.91        14.47        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95        45.47        53.00        23.61        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        28.73        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        30.64        15.06        31.79        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.66        19.27         3.12        17.00         5.88        24.07 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       12.43        11.61        15.95        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       34.82        15.55         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 
        2.01         5.10        36.20        20.35        15.78        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       12.89        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
        7.76         0.26        27.62        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
       12.03         0.69         9.83        12.43        14.93         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7649 
       10.85         1.08         0.23        12.95        49.38        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       19.82        23.80        15.65        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       43.79        15.81        21.30        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO 
       13.68         3.12         9.40         0.30        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.13              0.23 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            23.54             84.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             8.91             14.93 
[1] "0.1 - 23.5 (8.9)"  "0.2 - 84.1 (14.9)"
[1] "hr=" "2.8"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  3Q GAIN MUTATED         0        0        2         2        13         0
  3Q GAIN WILD-TYPE       1        6       11        24       104         5
                   vv
clus                STAGE IV
  3Q GAIN MUTATED          1
  3Q GAIN WILD-TYPE        3
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                2                11
  STAGE IIA               2                24
  STAGE IIB              13               104
  STAGE III               0                 5
  STAGE IV                1                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q GAIN MUTATED     0   3  15   0
  3Q GAIN WILD-TYPE   8  18 124   4
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               0                 8
  T2               3                18
  T3              15               124
  T4               0                 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"
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5  13
  3Q GAIN WILD-TYPE  40 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5   13
  3Q GAIN WILD-TYPE   40  111
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               5                40
  1              13               111
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    8  1
  3Q GAIN WILD-TYPE 72  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8    1
  3Q GAIN WILD-TYPE   72    3
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               8                72
  1               1                 3
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    5 13
  3Q GAIN WILD-TYPE 73 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5   13
  3Q GAIN WILD-TYPE   73   82
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               5                73
  MALE                13                82
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3Q GAIN MUTATED                                    17
  3Q GAIN WILD-TYPE                                 128
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3Q GAIN MUTATED                                       1
  3Q GAIN WILD-TYPE                                    21
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  3Q GAIN MUTATED                                                  0
  3Q GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  3Q GAIN MUTATED                                     0
  3Q GAIN WILD-TYPE                                   1
D6V8, multiclass
                                                  clus
vv                                                 3Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           17
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 3Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D6V9, continuous
D6V10, continuous
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED   10  7  0  1
  3Q GAIN WILD-TYPE 98 44  2  3
D6V11, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              10                98
  R1               7                44
  R2               0                 2
  RX               1                 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"
D6V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0    17
  3Q GAIN WILD-TYPE     3                         7   141
D6V13, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  17               141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0  15
  3Q GAIN WILD-TYPE   3 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   15
  3Q GAIN WILD-TYPE    3  120
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               120
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    7  3
  4P GAIN WILD-TYPE 72 89
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               161 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                89 
$`4P GAIN MUTATED`
TCGA-2J-AAB6 TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IS TCGA-3A-A9IV 
        9.63        11.84        45.47        68.52        30.64        31.79 
TCGA-FB-AAPP TCGA-HZ-7922 TCGA-HZ-8636 TCGA-YB-A89D 
       15.95         0.13        17.92        11.51 

$`4P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.72        22.26        31.86        15.91        14.47        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        53.00        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        28.73        60.95        84.10        63.85        50.70 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.70        19.46         7.10         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
        3.12        17.00         5.88        24.07        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       11.61        37.15         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       15.55         4.04         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 
        2.01         5.10        36.20        20.35        15.78        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       12.89        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
        7.76         0.26        27.62        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        4.77        21.90        15.35        19.82        23.80        15.65 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
        6.02        11.11         7.40         9.44         8.05        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.56         9.14        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        12.76        66.28         0.69 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.13              0.23 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            68.52             84.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           16.935            14.140 
[1] "0.1 - 68.5 (16.9)" "0.2 - 84.1 (14.1)"
[1] "hr=" "2.5"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  4P GAIN MUTATED         0        0        3         1         6         0
  4P GAIN WILD-TYPE       1        6       10        25       111         5
                   vv
clus                STAGE IV
  4P GAIN MUTATED          1
  4P GAIN WILD-TYPE        3
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                3                10
  STAGE IIA               1                25
  STAGE IIB               6               111
  STAGE III               0                 5
  STAGE IV                1                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     0   3   8   0
  4P GAIN WILD-TYPE   8  18 131   4
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                 8
  T2               3                18
  T3               8               131
  T4               0                 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"
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   6
  4P GAIN WILD-TYPE  41 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    6
  4P GAIN WILD-TYPE   41  118
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               4                41
  1               6               118
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 78  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   78    3
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               2                78
  1               1                 3
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    6  5
  4P GAIN WILD-TYPE 72 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    5
  4P GAIN WILD-TYPE   72   90
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6                72
  MALE                 5                90
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4P GAIN MUTATED                                     6
  4P GAIN WILD-TYPE                                 139
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4P GAIN MUTATED                                       4
  4P GAIN WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  4P GAIN MUTATED                                                  0
  4P GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  4P GAIN MUTATED                                     1
  4P GAIN WILD-TYPE                                   0
D7V8, multiclass
                                                  clus
vv                                                 4P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 4P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            139
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D7V9, continuous
D7V10, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     8   3   0   0
  4P GAIN WILD-TYPE 100  48   2   4
D7V11, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               8               100
  R1               3                48
  R2               0                 2
  RX               0                 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"
D7V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         0    11
  4P GAIN WILD-TYPE     3                         7   147
D7V13, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  11               147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   7
  4P GAIN WILD-TYPE   2 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    7
  4P GAIN WILD-TYPE    2  128
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               7               128
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    6  2
  4Q GAIN WILD-TYPE 73 90
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               163 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                90 
$`4Q GAIN MUTATED`
TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IS TCGA-3A-A9IV TCGA-FB-AAPP TCGA-HZ-7922 
       45.47        68.52        30.64        31.79        15.95         0.13 
TCGA-HZ-8636 TCGA-YB-A89D 
       17.92        11.51 

$`4Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
       22.49         3.39        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       63.85        50.70        15.06        34.09        10.13        12.39 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.66        19.27         3.12        17.00         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       14.76        12.43        11.61        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        8.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
       15.78        17.79        12.89        13.84        22.06        21.73 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
        0.92        19.50         7.76         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       12.95        49.38         4.77        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       23.80        15.65        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        8.05        13.28         7.56         9.14        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        27.75        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH 
       13.81        12.99        12.03        13.32        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.13              0.23 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            68.52             84.10 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            24.28             13.84 
[1] "0.1 - 68.5 (24.3)" "0.2 - 84.1 (13.8)"
[1] "hr=" "3.5"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  4Q GAIN MUTATED         0        0        3         0         4         0
  4Q GAIN WILD-TYPE       1        6       10        26       113         5
                   vv
clus                STAGE IV
  4Q GAIN MUTATED          1
  4Q GAIN WILD-TYPE        3
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                3                10
  STAGE IIA               0                26
  STAGE IIB               4               113
  STAGE III               0                 5
  STAGE IV                1                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     0   3   5   0
  4Q GAIN WILD-TYPE   8  18 134   4
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                 8
  T2               3                18
  T3               5               134
  T4               0                 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"
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3   4
  4Q GAIN WILD-TYPE  42 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    4
  4Q GAIN WILD-TYPE   42  120
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               3                42
  1               4               120
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  1
  4Q GAIN WILD-TYPE 80  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    1
  4Q GAIN WILD-TYPE   80    3
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               0                80
  1               1                 3
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    4  4
  4Q GAIN WILD-TYPE 74 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    4
  4Q GAIN WILD-TYPE   74   91
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4                74
  MALE                 4                91
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4Q GAIN MUTATED                                     4
  4Q GAIN WILD-TYPE                                 141
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4Q GAIN MUTATED                                       4
  4Q GAIN WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  4Q GAIN MUTATED                                                  0
  4Q GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  4Q GAIN MUTATED                                     0
  4Q GAIN WILD-TYPE                                   1
D8V8, multiclass
                                                  clus
vv                                                 4Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 4Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            141
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D8V9, continuous
D8V10, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     5   3   0   0
  4Q GAIN WILD-TYPE 103  48   2   4
D8V11, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               103
  R1               3                48
  R2               0                 2
  RX               0                 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"
D8V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         0     8
  4Q GAIN WILD-TYPE     3                         7   150
D8V13, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   8               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   7
  4Q GAIN WILD-TYPE   3 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    7
  4Q GAIN WILD-TYPE    3  128
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               7               128
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   13 13
  5P GAIN WILD-TYPE 66 79
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               26               145 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               13                79 
$`5P GAIN MUTATED`
TCGA-2J-AABF TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IN 
       22.72        11.84         9.11        45.47        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-AAPP 
       63.85        30.64        31.79         3.12        14.76        15.95 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-A77O 
       23.54        15.55         4.04        21.73         0.13         5.26 
TCGA-IB-7886 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7LX TCGA-LB-A7SX TCGA-M8-A5N4 
        4.04        15.85         1.35         8.22        12.92        19.20 
TCGA-OE-A75W TCGA-YH-A8SY 
        8.78        12.76 

$`5P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.26        31.86        15.91        14.47        14.40 
TCGA-2J-AABT TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       10.49        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       28.73        60.95        50.70        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       12.39        75.12        71.74        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.10         7.66        19.27        17.00         5.88        24.07 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       12.43        11.61        37.15         7.50        12.53        34.82 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        5.03         1.02         8.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 
       22.06         0.92        19.50         7.76         0.26        27.62 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       20.19        17.03        23.21        12.03         0.69         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q 
       16.14        10.13         6.38        21.60        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        0.23        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 
       19.82        23.80        15.65        41.33         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       17.16        12.00         7.20        15.12        20.88        21.90 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       11.11         7.40         9.44         8.05        13.28         7.56 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
        9.14        12.46        10.29        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        27.75        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YY-A8LH 
       13.81        12.99        12.03        13.32        11.51        66.28 
TCGA-Z5-AAPL 
        0.69 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.13              0.23 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            84.10             75.12 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           15.155            14.140 
[1] "0.1 - 84.1 (15.2)" "0.2 - 75.1 (14.1)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  5P GAIN MUTATED         1        0        4         4        16         1
  5P GAIN WILD-TYPE       0        6        9        22       101         4
                   vv
clus                STAGE IV
  5P GAIN MUTATED          0
  5P GAIN WILD-TYPE        4
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 6
  STAGE IB                4                 9
  STAGE IIA               4                22
  STAGE IIB              16               101
  STAGE III               1                 4
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P GAIN MUTATED     1   6  19   0
  5P GAIN WILD-TYPE   7  15 120   4
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                 7
  T2               6                15
  T3              19               120
  T4               0                 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"
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     7  17
  5P GAIN WILD-TYPE  38 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   17
  5P GAIN WILD-TYPE   38  107
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               7                38
  1              17               107
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   10  0
  5P GAIN WILD-TYPE 70  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     10    0
  5P GAIN WILD-TYPE   70    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              10                70
  1               0                 4
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   10 17
  5P GAIN WILD-TYPE 68 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     10   17
  5P GAIN WILD-TYPE   68   78
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              10                68
  MALE                17                78
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5P GAIN MUTATED                                    18
  5P GAIN WILD-TYPE                                 127
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5P GAIN MUTATED                                       7
  5P GAIN WILD-TYPE                                    15
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  5P GAIN MUTATED                                                  0
  5P GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  5P GAIN MUTATED                                     1
  5P GAIN WILD-TYPE                                   0
D9V8, multiclass
                                                  clus
vv                                                 5P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 5P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D9V9, continuous
D9V10, continuous
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   15 10  0  1
  5P GAIN WILD-TYPE 93 41  2  3
D9V11, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              15                93
  R1              10                41
  R2               0                 2
  RX               1                 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"
D9V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         1    25
  5P GAIN WILD-TYPE     3                         6   133
D9V13, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  25               133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  19
  5P GAIN WILD-TYPE   2 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   19
  5P GAIN WILD-TYPE    2  116
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              19               116
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   11  8
  5Q GAIN WILD-TYPE 68 84
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               152 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                84 
$`5Q GAIN MUTATED`
TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IV 
       45.47        84.10        68.52        63.85        30.64        31.79 
TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
        3.12        14.76        15.95        23.54        15.55         4.04 
TCGA-HZ-7922 TCGA-HZ-A77O TCGA-IB-7886 TCGA-IB-A5SP TCGA-IB-A7LX TCGA-LB-A7SX 
        0.13         5.26         4.04        15.85         8.22        12.92 
TCGA-M8-A5N4 
       19.20 

$`5Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
       22.49         3.39        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR 
       20.84         7.36        24.26        28.73        60.95        50.70 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.70        19.46         7.10         7.66        19.27 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ 
       17.00         5.88        24.07        12.43        11.61        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
        7.50        12.53        34.82         5.03         1.02         8.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 
       24.36         2.01         5.10        36.20        20.35        15.78 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
       17.79        12.89        13.84        22.06        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
       19.50         7.76         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       14.93        17.92         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
        6.38        21.60        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       15.65        41.33         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 
        7.20        15.12        20.88        21.90         1.35        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        27.75        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.13              0.23 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            84.10             75.12 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           15.850            13.825 
[1] "0.1 - 84.1 (15.8)" "0.2 - 75.1 (13.8)"
[1] "hr=" "1.7"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  5Q GAIN MUTATED         1        0        4         3        11         0
  5Q GAIN WILD-TYPE       0        6        9        23       106         5
                   vv
clus                STAGE IV
  5Q GAIN MUTATED          0
  5Q GAIN WILD-TYPE        4
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 6
  STAGE IB                4                 9
  STAGE IIA               3                23
  STAGE IIB              11               106
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED     1   6  12   0
  5Q GAIN WILD-TYPE   7  15 127   4
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               1                 7
  T2               6                15
  T3              12               127
  T4               0                 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"
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     6  11
  5Q GAIN WILD-TYPE  39 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      6   11
  5Q GAIN WILD-TYPE   39  113
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               6                39
  1              11               113
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    5  0
  5Q GAIN WILD-TYPE 75  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    0
  5Q GAIN WILD-TYPE   75    4
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               5                75
  1               0                 4
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    8 12
  5Q GAIN WILD-TYPE 70 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8   12
  5Q GAIN WILD-TYPE   70   83
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               8                70
  MALE                12                83
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5Q GAIN MUTATED                                    14
  5Q GAIN WILD-TYPE                                 131
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5Q GAIN MUTATED                                       6
  5Q GAIN WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  5Q GAIN MUTATED                                                  0
  5Q GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  5Q GAIN MUTATED                                     0
  5Q GAIN WILD-TYPE                                   1
D10V8, multiclass
                                                  clus
vv                                                 5Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           14
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 5Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            131
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D10V9, continuous
D10V10, continuous
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED   12  8  0  0
  5Q GAIN WILD-TYPE 96 43  2  4
D10V11, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              12                96
  R1               8                43
  R2               0                 2
  RX               0                 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"
D10V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         1    18
  5Q GAIN WILD-TYPE     3                         6   140
D10V13, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  18               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  15
  5Q GAIN WILD-TYPE   2 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   15
  5Q GAIN WILD-TYPE    2  120
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              15               120
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    4  2
  6P GAIN WILD-TYPE 75 90
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6               165 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                90 
$`6P GAIN MUTATED`
TCGA-2J-AABF TCGA-3A-A9IO TCGA-FB-AAPZ TCGA-HZ-8005 TCGA-LB-A8F3 TCGA-US-A776 
       22.72        63.85        23.54         3.95        12.46        27.75 

$`6P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.26        31.86        15.91        14.47        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
        3.39        12.95         9.60        45.47        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP 
        5.88        24.07        14.76        12.43        11.61        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        34.82        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        5.03         1.02         8.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       22.06        21.73         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        0.69         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       21.90        15.35        19.82        23.80        15.65        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       11.11         7.40         9.44         8.05        13.28         7.56 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        9.14        12.92        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       13.68         3.12        15.32         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       17.26        23.08        22.85        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             3.95              0.13 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            63.85             84.10 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            23.13             14.14 
[1] "4.0 - 63.9 (23.1)" "0.1 - 84.1 (14.1)"
[1] "hr=" "2.6"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  6P GAIN MUTATED         0        0        0         2         3         0
  6P GAIN WILD-TYPE       1        6       13        24       114         5
                   vv
clus                STAGE IV
  6P GAIN MUTATED          0
  6P GAIN WILD-TYPE        4
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                0                13
  STAGE IIA               2                24
  STAGE IIB               3               114
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED     0   1   4   0
  6P GAIN WILD-TYPE   8  20 135   4
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               0                 8
  T2               1                20
  T3               4               135
  T4               0                 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"
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2   3
  6P GAIN WILD-TYPE  43 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    3
  6P GAIN WILD-TYPE   43  121
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               2                43
  1               3               121
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    1  0
  6P GAIN WILD-TYPE 79  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    0
  6P GAIN WILD-TYPE   79    4
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               1                79
  1               0                 4
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    1  5
  6P GAIN WILD-TYPE 77 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    5
  6P GAIN WILD-TYPE   77   90
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               1                77
  MALE                 5                90
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6P GAIN MUTATED                                     4
  6P GAIN WILD-TYPE                                 141
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6P GAIN MUTATED                                       1
  6P GAIN WILD-TYPE                                    21
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  6P GAIN MUTATED                                                  1
  6P GAIN WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  6P GAIN MUTATED                                     0
  6P GAIN WILD-TYPE                                   1
D11V8, multiclass
                                                  clus
vv                                                 6P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 6P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            141
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D11V9, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                53 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IX 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F2-6880        TCGA-F2-A8YN        TCGA-FB-A4P5        TCGA-FB-A5VM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-7886 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-YY-A8LH 
"6P GAIN WILD-TYPE" 
D11V10, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                44 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABI        TCGA-2J-AABO 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IR        TCGA-3A-A9IX 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUV 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YY-A8LH 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED     4   2   0   0
  6P GAIN WILD-TYPE 104  49   2   4
D11V11, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               4               104
  R1               2                49
  R2               0                 2
  RX               0                 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"
D11V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                         1     5
  6P GAIN WILD-TYPE     3                         6   153
D11V13, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   5               153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0   5
  6P GAIN WILD-TYPE   3 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    5
  6P GAIN WILD-TYPE    3  130
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               130
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    2  2
  6Q GAIN WILD-TYPE 77 90
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               167 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                90 
$`6Q GAIN MUTATED`
TCGA-2J-AABF TCGA-3A-A9IO TCGA-HZ-8005 TCGA-LB-A8F3 
       22.72        63.85         3.95        12.46 

$`6Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.26        31.86        15.91        14.47        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
        3.39        12.95         9.60        45.47        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP 
        5.88        24.07        14.76        12.43        11.61        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       37.15         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
        4.04         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 
        5.10        36.20        20.35        15.78        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       13.84        22.06        21.73         0.92        19.50         7.76 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
        0.13         0.26        27.62        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        4.77        21.90        15.35        19.82        23.80        15.65 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
        6.02        11.11         7.40         9.44         8.05        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        7.56         9.14        12.92        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       15.45        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       14.14         0.39        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             3.95              0.13 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            63.85             84.10 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            17.59             14.17 
[1] "4.0 - 63.9 (17.6)" "0.1 - 84.1 (14.2)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  6Q GAIN MUTATED         0        0        0         1         2         0
  6Q GAIN WILD-TYPE       1        6       13        25       115         5
                   vv
clus                STAGE IV
  6Q GAIN MUTATED          0
  6Q GAIN WILD-TYPE        4
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                0                13
  STAGE IIA               1                25
  STAGE IIB               2               115
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED     0   0   3   0
  6Q GAIN WILD-TYPE   8  21 136   4
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               0                 8
  T2               0                21
  T3               3               136
  T4               0                 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"
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1   2
  6Q GAIN WILD-TYPE  44 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    2
  6Q GAIN WILD-TYPE   44  122
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               1                44
  1               2               122
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  0
  6Q GAIN WILD-TYPE 79  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    0
  6Q GAIN WILD-TYPE   79    4
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               1                79
  1               0                 4
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  3
  6Q GAIN WILD-TYPE 77 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    3
  6Q GAIN WILD-TYPE   77   92
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               1                77
  MALE                 3                92
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6Q GAIN MUTATED                                     3
  6Q GAIN WILD-TYPE                                 142
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6Q GAIN MUTATED                                       1
  6Q GAIN WILD-TYPE                                    21
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  6Q GAIN MUTATED                                                  0
  6Q GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  6Q GAIN MUTATED                                     0
  6Q GAIN WILD-TYPE                                   1
D12V8, multiclass
                                                  clus
vv                                                 6Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 6Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            142
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D12V9, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                53 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IX 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F2-6880        TCGA-F2-A8YN        TCGA-FB-A4P5        TCGA-FB-A5VM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-7886 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-YY-A8LH 
"6Q GAIN WILD-TYPE" 
D12V10, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                44 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABI        TCGA-2J-AABO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IR        TCGA-3A-A9IX 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YY-A8LH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED     2   2   0   0
  6Q GAIN WILD-TYPE 106  49   2   4
D12V11, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               2               106
  R1               2                49
  R2               0                 2
  RX               0                 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"
D12V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         1     3
  6Q GAIN WILD-TYPE     3                         6   155
D12V13, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   3               155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0   3
  6Q GAIN WILD-TYPE   3 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    3
  6Q GAIN WILD-TYPE    3  132
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3               132
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   22 28
  7P GAIN WILD-TYPE 57 64
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               50               121 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               28                64 
$`7P GAIN MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABP TCGA-2J-AABT 
        2.17         9.63         2.63        22.72        11.84        10.49 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
        9.60        45.47        60.95        84.10        68.52        63.85 
TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAPZ 
       31.79        12.39         3.12        24.07        15.95        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-H8-A6C1 TCGA-HZ-7289 
       15.55         4.04        24.36         5.10        22.06        21.73 
TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-IB-7645 TCGA-IB-7646 
       17.03         3.95        17.92         5.26        49.38         4.77 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP 
       23.80         4.04        15.81         3.85        17.16        15.85 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUQ TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX 
        1.35         8.22         6.02         8.05         9.14        12.92 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-US-A776 TCGA-US-A77E 
       12.46        19.20        15.32        21.24        27.75        14.14 
TCGA-YB-A89D TCGA-YY-A8LH 
       11.51        66.28 

$`7P GAIN WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI 
       23.97        20.61        19.96        22.22        22.26        31.86 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.91        14.47        14.40         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       22.49         3.39        12.95        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        28.73        50.70        30.64        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       34.09        10.13        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 
       19.46         7.10         7.66        19.27        17.00         5.88 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       14.76        12.43        11.61        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5920 TCGA-FZ-5922 
       34.82         5.03         1.02         8.02         2.01        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7918 
       20.35        15.78        17.79        12.89        13.84         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
       19.50         7.76         0.13         0.26        27.62        20.19 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         9.83        12.43        14.93 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7647 TCGA-IB-7649 
       10.85         1.08         0.23        12.95        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 
       19.82        15.65        41.33         3.62        43.79        19.66 
TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS 
       21.30        15.98         2.47        12.00         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88        21.90        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17        11.11         7.40         9.44        13.28         7.56 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M 
       10.29         8.78        15.45        13.68         3.12         9.40 
TCGA-RL-AAAS TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G 
        0.30        17.26        23.08        22.85        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY 
       18.67        13.81        12.99        12.03        13.32        12.76 
TCGA-Z5-AAPL 
        0.69 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.35              0.13 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            84.10             75.12 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           15.435            13.840 
[1] "1.4 - 84.1 (15.4)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  7P GAIN MUTATED         1        0        3         8        36         0
  7P GAIN WILD-TYPE       0        6       10        18        81         5
                   vv
clus                STAGE IV
  7P GAIN MUTATED          1
  7P GAIN WILD-TYPE        3
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 6
  STAGE IB                3                10
  STAGE IIA               8                18
  STAGE IIB              36                81
  STAGE III               0                 5
  STAGE IV                1                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    1  5 43  0
  7P GAIN WILD-TYPE  7 16 96  4
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               1                 7
  T2               5                16
  T3              43                96
  T4               0                 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"
D13V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   11 36
  7P GAIN WILD-TYPE 34 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     11   36
  7P GAIN WILD-TYPE   34   88
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              11                34
  1              36                88
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   22  1
  7P GAIN WILD-TYPE 58  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     22    1
  7P GAIN WILD-TYPE   58    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              22                58
  1               1                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   19 31
  7P GAIN WILD-TYPE 59 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     19   31
  7P GAIN WILD-TYPE   59   64
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              19                59
  MALE                31                64
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  7P GAIN MUTATED                                    37
  7P GAIN WILD-TYPE                                 108
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  7P GAIN MUTATED                                      11
  7P GAIN WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  7P GAIN MUTATED                                                  1
  7P GAIN WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  7P GAIN MUTATED                                     1
  7P GAIN WILD-TYPE                                   0
D13V8, multiclass
                                                  clus
vv                                                 7P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           37
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 7P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            108
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D13V9, continuous
D13V10, continuous
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   25 18  1  3
  7P GAIN WILD-TYPE 83 33  1  1
D13V11, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              25                83
  R1              18                33
  R2               1                 1
  RX               3                 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"
D13V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       1                         3    43
  7P GAIN WILD-TYPE     2                         4   115
D13V13, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  43               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    0 37
  7P GAIN WILD-TYPE  3 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0   37
  7P GAIN WILD-TYPE    3   98
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              37                98
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   18 29
  7Q GAIN WILD-TYPE 61 63
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               47               124 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               29                63 
$`7Q GAIN MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABP TCGA-2J-AABT 
        2.17         9.63         2.63        22.72        11.84        10.49 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        9.60        45.47        20.84        60.95        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPP 
       63.85        31.79        12.39         3.12        24.07        15.95 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-HZ-7289 TCGA-HZ-7926 
       15.55         4.04        24.36         5.10        21.73        17.03 
TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7652 
        3.95        17.92         5.26        49.38         4.77        23.80 
TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A6UG TCGA-IB-A7LX 
        4.04        15.81         3.85        17.16         1.35         8.22 
TCGA-IB-AAUQ TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 
        6.02         8.05         9.14        12.92        12.46        19.20 
TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-US-A776 TCGA-US-A77E TCGA-YB-A89D 
       15.32        21.24        27.75        14.14        11.51 

$`7Q GAIN WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI 
       23.97        20.61        19.96        22.22        22.26        31.86 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.91        14.47        14.40         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB 
       22.49         3.39        12.95        53.00        23.61         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       24.26        28.73        50.70        30.64        15.06        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       10.13        75.12        71.74        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM 
        7.10         7.66        19.27        17.00         5.88        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       12.43        11.61        37.15         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5920 TCGA-FZ-5922 
       23.54         5.03         1.02         8.02         2.01        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       20.35        15.78        17.79        12.89        13.84        22.06 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
        0.92        19.50         7.76         0.13         0.26        27.62 
TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       20.19        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93         4.96        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7647 
       21.60        10.85         1.08         0.23        12.95        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 
       15.35        19.82        15.65        41.33         3.62        43.79 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.66        21.30        15.98         2.47        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        15.12        20.88        21.90        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        4.73         7.86        14.17        11.11         7.40         9.44 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       13.28         7.56        10.29         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        3.12         9.40         0.30        17.26        23.08        22.85 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        12.76        66.28         0.69 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.35              0.13 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            84.10             75.12 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           14.140            14.285 
[1] "1.4 - 84.1 (14.1)" "0.1 - 75.1 (14.3)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  7Q GAIN MUTATED         1        0        3         7        34         0
  7Q GAIN WILD-TYPE       0        6       10        19        83         5
                   vv
clus                STAGE IV
  7Q GAIN MUTATED          1
  7Q GAIN WILD-TYPE        3
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 6
  STAGE IB                3                10
  STAGE IIA               7                19
  STAGE IIB              34                83
  STAGE III               0                 5
  STAGE IV                1                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    1  4 41  0
  7Q GAIN WILD-TYPE  7 17 98  4
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               1                 7
  T2               4                17
  T3              41                98
  T4               0                 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"
D14V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   10 34
  7Q GAIN WILD-TYPE 35 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     10   34
  7Q GAIN WILD-TYPE   35   90
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              10                35
  1              34                90
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   21  1
  7Q GAIN WILD-TYPE 59  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     21    1
  7Q GAIN WILD-TYPE   59    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              21                59
  1               1                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   18 29
  7Q GAIN WILD-TYPE 60 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     18   29
  7Q GAIN WILD-TYPE   60   66
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              18                60
  MALE                29                66
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  7Q GAIN MUTATED                                    35
  7Q GAIN WILD-TYPE                                 110
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  7Q GAIN MUTATED                                      10
  7Q GAIN WILD-TYPE                                    12
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  7Q GAIN MUTATED                                                  1
  7Q GAIN WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  7Q GAIN MUTATED                                     1
  7Q GAIN WILD-TYPE                                   0
D14V8, multiclass
                                                  clus
vv                                                 7Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           35
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 7Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            110
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           12
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D14V9, continuous
D14V10, continuous
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   23 17  1  3
  7Q GAIN WILD-TYPE 85 34  1  1
D14V11, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              23                85
  R1              17                34
  R2               1                 1
  RX               3                 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"
D14V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       1                         3    40
  7Q GAIN WILD-TYPE     2                         4   118
D14V13, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  40               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     0  35
  7Q GAIN WILD-TYPE   3 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0   35
  7Q GAIN WILD-TYPE    3  100
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              35               100
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   12 11
  8P GAIN WILD-TYPE 67 81
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               23               148 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                81 
$`8P GAIN MUTATED`
TCGA-2J-AABF TCGA-2J-AABH TCGA-3A-A9I5 TCGA-3A-A9IO TCGA-3A-A9IS TCGA-FB-A545 
       22.72        22.26        53.00        63.85        30.64        24.07 
TCGA-FB-AAPP TCGA-FB-AAQ1 TCGA-FZ-5921 TCGA-HZ-7922 TCGA-HZ-8315 TCGA-HZ-A77O 
       15.95         4.04         5.10         0.13         9.83         5.26 
TCGA-IB-7646 TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG 
        4.77         4.04         3.85        15.85        21.90         1.35 
TCGA-M8-A5N4 TCGA-S4-A8RM TCGA-S4-A8RO TCGA-YB-A89D TCGA-YH-A8SY 
       19.20        21.24        17.26        11.51        12.76 

$`8P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABR 
       22.22        31.86        15.91        14.47        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IR 
       24.26        28.73        60.95        84.10        68.52        50.70 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        31.79        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T 
       19.27         3.12        17.00         5.88        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       11.61        37.15         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       22.06        21.73         0.92        19.50         7.76         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        3.95        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q 
       16.14        10.13         6.38        21.60        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
        0.23        12.95        49.38        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       23.80        15.65        41.33         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       19.66        21.30        15.98         2.47        17.16        12.00 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        15.12        20.88         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX 
        9.44         8.05        13.28         7.56         9.14        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
       15.32         9.40         0.30        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        66.28         0.69 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.13              0.23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            63.85             84.10 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           15.850            14.155 
[1] "0.1 - 63.9 (15.8)" "0.2 - 84.1 (14.2)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  8P GAIN MUTATED         0        1        1         5        15         1
  8P GAIN WILD-TYPE       1        5       12        21       102         4
                   vv
clus                STAGE IV
  8P GAIN MUTATED          0
  8P GAIN WILD-TYPE        4
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 5
  STAGE IB                1                12
  STAGE IIA               5                21
  STAGE IIB              15               102
  STAGE III               1                 4
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED     1   2  20   0
  8P GAIN WILD-TYPE   7  19 119   4
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               1                 7
  T2               2                19
  T3              20               119
  T4               0                 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"
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     7  16
  8P GAIN WILD-TYPE  38 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      7   16
  8P GAIN WILD-TYPE   38  108
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               7                38
  1              16               108
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   11  0
  8P GAIN WILD-TYPE 69  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     11    0
  8P GAIN WILD-TYPE   69    4
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              11                69
  1               0                 4
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    9 15
  8P GAIN WILD-TYPE 69 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   15
  8P GAIN WILD-TYPE   69   80
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               9                69
  MALE                15                80
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8P GAIN MUTATED                                    20
  8P GAIN WILD-TYPE                                 125
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8P GAIN MUTATED                                       3
  8P GAIN WILD-TYPE                                    19
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  8P GAIN MUTATED                                                  0
  8P GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  8P GAIN MUTATED                                     0
  8P GAIN WILD-TYPE                                   1
D15V8, multiclass
                                                  clus
vv                                                 8P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           20
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 8P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D15V9, continuous
D15V10, continuous
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED   11 10  0  0
  8P GAIN WILD-TYPE 97 41  2  4
D15V11, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              11                97
  R1              10                41
  R2               0                 2
  RX               0                 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"
D15V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         0    22
  8P GAIN WILD-TYPE     3                         7   136
D15V13, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  22               136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1  18
  8P GAIN WILD-TYPE   2 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   18
  8P GAIN WILD-TYPE    2  117
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              18               117
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   18 26
  8Q GAIN WILD-TYPE 61 66
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               44               127 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               26                66 
$`8Q GAIN MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABP TCGA-2L-AAQI TCGA-2L-AAQJ 
       23.97        22.72        22.26        11.84         3.39        12.95 
TCGA-3A-A9I5 TCGA-3A-A9IB TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IX TCGA-3A-A9IZ 
       53.00         7.36        63.85        30.64        34.09        10.13 
TCGA-F2-6879 TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPU 
       10.98         3.12        24.07        12.43        15.95        12.53 
TCGA-FB-AAQ1 TCGA-FZ-5921 TCGA-FZ-5926 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8315 
        4.04         5.10        17.79         0.13        20.19         9.83 
TCGA-HZ-8636 TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7886 
       17.92         5.26         0.23         4.77        21.90         4.04 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG 
       19.66         3.85        17.16        15.85        21.90         1.35 
TCGA-IB-A7LX TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-S4-A8RM TCGA-S4-A8RO 
        8.22         9.14        19.20         8.78        21.24        17.26 
TCGA-YB-A89D TCGA-YH-A8SY 
       11.51        12.76 

$`8Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU 
       31.86        15.91        14.47        14.40        10.49         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 
       21.44         4.70        22.49         9.60        45.47        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
       20.84        24.26        28.73        60.95        84.10        68.52 
TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       50.70        15.06        31.79        12.39        75.12        71.74 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN 
        9.70        19.46         7.10         7.66        19.27        17.00 
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPY 
        5.88        14.76        11.61        37.15         7.50        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       23.54        15.55         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-H6-8124 TCGA-H6-A45N 
        2.01        36.20        20.35        15.78        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       22.06        21.73         0.92        19.50         7.76         0.26 
TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       27.62        17.03        23.21        12.03         0.69         3.95 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 
        6.38        21.60        10.85         1.08        12.95        49.38 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 
       15.35        19.82        23.80        15.65        41.33         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
       43.79        15.81        21.30        15.98         2.47        12.00 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
        7.20        15.12        20.88        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
        8.05        13.28         7.56        12.92        12.46        10.29 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       15.45        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YY-A8LH 
       18.67        13.81        12.99        12.03        13.32        66.28 
TCGA-Z5-AAPL 
        0.69 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.13              0.26 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            63.85             84.10 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           12.645            14.470 
[1] "0.1 - 63.9 (12.6)" "0.3 - 84.1 (14.5)"
[1] "hr=" "1.3"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  8Q GAIN MUTATED         0        2        3         7        28         3
  8Q GAIN WILD-TYPE       1        4       10        19        89         2
                   vv
clus                STAGE IV
  8Q GAIN MUTATED          1
  8Q GAIN WILD-TYPE        3
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                2                 4
  STAGE IB                3                10
  STAGE IIA               7                19
  STAGE IIB              28                89
  STAGE III               3                 2
  STAGE IV                1                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q GAIN MUTATED     2   5  36   1
  8Q GAIN WILD-TYPE   6  16 103   3
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               2                 6
  T2               5                16
  T3              36               103
  T4               1                 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"
D16V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   14 30
  8Q GAIN WILD-TYPE 31 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14   30
  8Q GAIN WILD-TYPE   31   94
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              14                31
  1              30                94
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   22  1
  8Q GAIN WILD-TYPE 58  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     22    1
  8Q GAIN WILD-TYPE   58    3
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              22                58
  1               1                 3
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   17 28
  8Q GAIN WILD-TYPE 61 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     17   28
  8Q GAIN WILD-TYPE   61   67
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              17                61
  MALE                28                67
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8Q GAIN MUTATED                                    38
  8Q GAIN WILD-TYPE                                 107
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8Q GAIN MUTATED                                       5
  8Q GAIN WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  8Q GAIN MUTATED                                                  0
  8Q GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  8Q GAIN MUTATED                                     1
  8Q GAIN WILD-TYPE                                   0
D16V8, multiclass
                                                  clus
vv                                                 8Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           38
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 8Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            107
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D16V9, continuous
D16V10, continuous
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   23 18  1  0
  8Q GAIN WILD-TYPE 85 33  1  4
D16V11, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              23                85
  R1              18                33
  R2               1                 1
  RX               0                 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"
D16V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       1                         0    41
  8Q GAIN WILD-TYPE     2                         7   117
D16V13, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  41               117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     2  31
  8Q GAIN WILD-TYPE   1 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2   31
  8Q GAIN WILD-TYPE    1  104
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              31               104
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    4  3
  9P GAIN WILD-TYPE 75 89
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               164 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                89 
$`9P GAIN MUTATED`
TCGA-2J-AABP TCGA-2L-AAQM TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-IB-7646 TCGA-IB-7893 
       11.84        45.47        15.95        23.54         4.77         3.85 
TCGA-M8-A5N4 
       19.20 

$`9P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        28.73        60.95        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ 
        5.88        24.07        14.76        12.43        11.61        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        34.82        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       20.35        15.78        17.79        12.89        13.84        22.06 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       21.73         0.92        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        3.95         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
       10.85         1.08         0.23        12.95        49.38        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       15.35        19.82        23.80        15.65        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 
        3.62        43.79        15.81        19.66        21.30        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX 
        9.44         8.05        13.28         7.56         9.14        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        27.75        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             3.85              0.13 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            45.47             84.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           15.950            14.155 
[1] "3.9 - 45.5 (15.9)" "0.1 - 84.1 (14.2)"
[1] "hr=" "1.4"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  9P GAIN MUTATED         0        0        0         2         5         0
  9P GAIN WILD-TYPE       1        6       13        24       112         5
                   vv
clus                STAGE IV
  9P GAIN MUTATED          0
  9P GAIN WILD-TYPE        4
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                0                13
  STAGE IIA               2                24
  STAGE IIB               5               112
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED     0   1   6   0
  9P GAIN WILD-TYPE   8  20 133   4
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               0                 8
  T2               1                20
  T3               6               133
  T4               0                 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"
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   5
  9P GAIN WILD-TYPE  43 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    5
  9P GAIN WILD-TYPE   43  119
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               2                43
  1               5               119
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    4  0
  9P GAIN WILD-TYPE 76  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4    0
  9P GAIN WILD-TYPE   76    4
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               4                76
  1               0                 4
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  5
  9P GAIN WILD-TYPE 76 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    5
  9P GAIN WILD-TYPE   76   90
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                76
  MALE                 5                90
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9P GAIN MUTATED                                     5
  9P GAIN WILD-TYPE                                 140
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9P GAIN MUTATED                                       1
  9P GAIN WILD-TYPE                                    21
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  9P GAIN MUTATED                                                  0
  9P GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  9P GAIN MUTATED                                     1
  9P GAIN WILD-TYPE                                   0
D17V8, multiclass
                                                  clus
vv                                                 9P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 9P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            140
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D17V9, continuous
D17V10, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED     4   3   0   0
  9P GAIN WILD-TYPE 104  48   2   4
D17V11, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               4               104
  R1               3                48
  R2               0                 2
  RX               0                 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"
D17V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         0     6
  9P GAIN WILD-TYPE     3                         7   152
D17V13, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   6               152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0   4
  9P GAIN WILD-TYPE   3 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    4
  9P GAIN WILD-TYPE    3  131
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               131
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    6  5
  9Q GAIN WILD-TYPE 73 87
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               160 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                87 
$`9Q GAIN MUTATED`
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IV TCGA-FB-AAPP TCGA-FB-AAPZ 
        9.60        45.47        68.52        31.79        15.95        23.54 
TCGA-IB-7646 TCGA-IB-7893 TCGA-IB-A5SP TCGA-M8-A5N4 TCGA-US-A779 
        4.77         3.85        15.85        19.20        16.80 

$`9Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       22.49         3.39        12.95        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IO 
        7.36        24.26        28.73        60.95        84.10        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        30.64        15.06        34.09        10.13        12.39 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.66        19.27         3.12        17.00         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       14.76        12.43        11.61        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       34.82        15.55         4.04         5.03         1.02         8.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 
       24.36         2.01         5.10        36.20        20.35        15.78 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
       17.79        12.89        13.84        22.06        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
       19.50         7.76         0.13         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
       12.43        14.93        17.92         4.96        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
        0.23        12.95        49.38        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       23.80        15.65        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       15.81        19.66        21.30        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
        6.02        11.11         7.40         9.44         8.05        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.56         9.14        12.92        12.46        10.29         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       15.45        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E 
       21.24        17.26        23.08        22.85        27.75        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             3.85              0.13 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            68.52             84.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           16.800            13.825 
[1] "3.9 - 68.5 (16.8)" "0.1 - 84.1 (13.8)"
[1] "hr=" "1.6"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  9Q GAIN MUTATED         0        0        2         3         6         0
  9Q GAIN WILD-TYPE       1        6       11        23       111         5
                   vv
clus                STAGE IV
  9Q GAIN MUTATED          0
  9Q GAIN WILD-TYPE        4
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                2                11
  STAGE IIA               3                23
  STAGE IIB               6               111
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED     0   3   8   0
  9Q GAIN WILD-TYPE   8  18 131   4
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               0                 8
  T2               3                18
  T3               8               131
  T4               0                 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"
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     4   6
  9Q GAIN WILD-TYPE  41 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    6
  9Q GAIN WILD-TYPE   41  118
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               4                41
  1               6               118
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  0
  9Q GAIN WILD-TYPE 76  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    0
  9Q GAIN WILD-TYPE   76    4
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               4                76
  1               0                 4
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  7
  9Q GAIN WILD-TYPE 74 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    7
  9Q GAIN WILD-TYPE   74   88
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               4                74
  MALE                 7                88
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9Q GAIN MUTATED                                     8
  9Q GAIN WILD-TYPE                                 137
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9Q GAIN MUTATED                                       3
  9Q GAIN WILD-TYPE                                    19
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  9Q GAIN MUTATED                                                  0
  9Q GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  9Q GAIN MUTATED                                     0
  9Q GAIN WILD-TYPE                                   1
D18V8, multiclass
                                                  clus
vv                                                 9Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 9Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            137
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D18V9, continuous
D18V10, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED     5   5   0   1
  9Q GAIN WILD-TYPE 103  46   2   3
D18V11, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               5               103
  R1               5                46
  R2               0                 2
  RX               1                 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"
D18V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         0    10
  9Q GAIN WILD-TYPE     3                         7   148
D18V13, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  10               148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0   7
  9Q GAIN WILD-TYPE   3 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    7
  9Q GAIN WILD-TYPE    3  128
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               7               128
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    4  4
  10P GAIN WILD-TYPE 75 88
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                163 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 88 
$`10P GAIN MUTATED`
TCGA-2L-AAQL TCGA-3A-A9IO TCGA-F2-A7TX TCGA-FZ-5920 TCGA-IB-A5SP TCGA-IB-AAUU 
        9.60        63.85         3.12         2.01        15.85         8.05 
TCGA-LB-A7SX TCGA-LB-A8F3 
       12.92        12.46 

$`10P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
       22.49         3.39        12.95        45.47        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 
       19.46         7.10         7.66        19.27        17.00         5.88 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ 
       24.07        14.76        12.43        11.61        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
        7.50        12.53        34.82        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02         8.02        24.36         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       20.35        15.78        17.79        12.89        13.84        22.06 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       21.73         0.92        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        3.95         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       21.90        15.35        19.82        23.80        15.65        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ 
        3.85        15.98         2.47        17.16        12.00         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A9Q5 
        7.40         9.44        13.28         7.56         9.14        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        9.40         0.30        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       27.75        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              2.01               0.13 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             63.85              84.10 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             11.03              14.47 
[1] "2.0 - 63.9 (11.0)" "0.1 - 84.1 (14.5)"
[1] "hr=" "1.3"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  10P GAIN MUTATED         0        0        0         2         5         0
  10P GAIN WILD-TYPE       1        6       13        24       112         5
                    vv
clus                 STAGE IV
  10P GAIN MUTATED          0
  10P GAIN WILD-TYPE        4
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                2                 24
  STAGE IIB                5                112
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED     0   0   7   0
  10P GAIN WILD-TYPE   8  21 132   4
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  8
  T2                0                 21
  T3                7                132
  T4                0                  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"
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2   5
  10P GAIN WILD-TYPE  43 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    5
  10P GAIN WILD-TYPE   43  119
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                2                 43
  1                5                119
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4  0
  10P GAIN WILD-TYPE 76  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    0
  10P GAIN WILD-TYPE   76    4
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                4                 76
  1                0                  4
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  6
  10P GAIN WILD-TYPE 76 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    6
  10P GAIN WILD-TYPE   76   89
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                2                 76
  MALE                  6                 89
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10P GAIN MUTATED                                     7
  10P GAIN WILD-TYPE                                 138
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10P GAIN MUTATED                                       1
  10P GAIN WILD-TYPE                                    21
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  10P GAIN MUTATED                                                  0
  10P GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  10P GAIN MUTATED                                     0
  10P GAIN WILD-TYPE                                   1
D19V8, multiclass
                                                  clus
vv                                                 10P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 10P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             138
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D19V9, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 52 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABI         TCGA-2J-AABO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2J-AABV         TCGA-2L-AAQA         TCGA-2L-AAQE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-3A-A9I9         TCGA-3A-A9IB         TCGA-3A-A9IJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-6880         TCGA-F2-A8YN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H6-A45N 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7886 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8126 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-IB-AAUV 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-XD-AAUL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"10P GAIN WILD-TYPE" 
D19V10, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 44 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2J-AABI         TCGA-2J-AABO         TCGA-3A-A9IB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-3A-A9IJ         TCGA-3A-A9IR         TCGA-3A-A9IX 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H8-A6C1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7891 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUT 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-US-A774         TCGA-XD-AAUI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-YY-A8LH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED     4   3   0   1
  10P GAIN WILD-TYPE 104  48   2   3
D19V11, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                4                104
  R1                3                 48
  R2                0                  2
  RX                1                  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"
D19V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         3     5
  10P GAIN WILD-TYPE     3                         4   153
D19V13, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                3                  4
  WHITE                                    5                153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0   5
  10P GAIN WILD-TYPE   3 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    5
  10P GAIN WILD-TYPE    3  130
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                130
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    4  8
  10Q GAIN WILD-TYPE 75 84
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                159 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                 84 
$`10Q GAIN MUTATED`
TCGA-2L-AAQL TCGA-3A-A9IO TCGA-F2-A7TX TCGA-FZ-5920 TCGA-FZ-5923 TCGA-IB-7886 
        9.60        63.85         3.12         2.01        20.35         4.04 
TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       15.85         1.35         8.22         8.05        12.92        12.46 

$`10Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
       22.49         3.39        12.95        45.47        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 
       19.46         7.10         7.66        19.27        17.00         5.88 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ 
       24.07        14.76        12.43        11.61        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
        7.50        12.53        34.82        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02         8.02        24.36         5.10        36.20 
TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
       15.78        17.79        12.89        13.84        22.06        21.73 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
        0.92        19.50         7.76         0.13         0.26        27.62 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       20.19        17.03        23.21        12.03         0.69         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 
       15.35        19.82        23.80        15.65        41.33         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        17.16        12.00         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
       21.90        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         9.44        13.28         7.56 
TCGA-L1-A7W4 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
        9.14        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO 
        3.12        15.32         9.40         0.30        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.35               0.13 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             63.85              84.10 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              8.91              14.76 
[1] "1.4 - 63.9 (8.9)"  "0.1 - 84.1 (14.8)"
[1] "hr=" "2"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  10Q GAIN MUTATED         0        0        0         2         8         0
  10Q GAIN WILD-TYPE       1        6       13        24       109         5
                    vv
clus                 STAGE IV
  10Q GAIN MUTATED          1
  10Q GAIN WILD-TYPE        3
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                2                 24
  STAGE IIB                8                109
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED     0   0  10   1
  10Q GAIN WILD-TYPE   8  21 129   3
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  8
  T2                0                 21
  T3               10                129
  T4                1                  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"
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2   9
  10Q GAIN WILD-TYPE  43 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    9
  10Q GAIN WILD-TYPE   43  115
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                2                 43
  1                9                115
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    6  1
  10Q GAIN WILD-TYPE 74  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    1
  10Q GAIN WILD-TYPE   74    3
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                6                 74
  1                1                  3
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2 10
  10Q GAIN WILD-TYPE 76 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   10
  10Q GAIN WILD-TYPE   76   85
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                 76
  MALE                 10                 85
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10Q GAIN MUTATED                                    11
  10Q GAIN WILD-TYPE                                 134
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10Q GAIN MUTATED                                       1
  10Q GAIN WILD-TYPE                                    21
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  10Q GAIN MUTATED                                                  0
  10Q GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  10Q GAIN MUTATED                                     0
  10Q GAIN WILD-TYPE                                   1
D20V8, multiclass
                                                  clus
vv                                                 10Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 10Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             134
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D20V9, continuous
D20V10, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     6   5   0   1
  10Q GAIN WILD-TYPE 102  46   2   3
D20V11, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                6                102
  R1                5                 46
  R2                0                  2
  RX                1                  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"
D20V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         3     9
  10Q GAIN WILD-TYPE     3                         4   149
D20V13, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                3                  4
  WHITE                                    9                149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   9
  10Q GAIN WILD-TYPE   3 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    9
  10Q GAIN WILD-TYPE    3  126
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                9                126
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    5  8
  11P GAIN WILD-TYPE 74 84
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                158 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                 84 
$`11P GAIN MUTATED`
TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-HZ-A4BH TCGA-IB-7647 
        3.12        24.07        15.55         4.04         6.38        21.90 
TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7LX TCGA-M8-A5N4 
        3.85        17.16        15.85         1.35         8.22        19.20 
TCGA-US-A776 
       27.75 

$`11P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 
       22.49         3.39        12.95         9.60        45.47        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       23.61        20.84         7.36        24.26        28.73        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       84.10        68.52        63.85        50.70        30.64        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       31.79        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.70        19.46         7.10         7.66        19.27 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP 
       17.00         5.88        14.76        12.43        11.61        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ2 
       37.15         7.50        12.53        34.82        23.54         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       20.35        15.78        17.79        12.89        13.84        22.06 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       21.73         0.92        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        3.95         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       21.70        16.14        10.13        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7649 
        1.08         0.23        12.95        49.38         4.77        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       19.82        23.80        15.65        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 
       43.79        15.81        19.66        21.30        15.98         2.47 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 
       12.00         7.20        15.12        20.88        21.90        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.92        12.46        10.29         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO 
        3.12        15.32         9.40         0.30        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       23.08        22.85        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.35               0.13 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             27.75              84.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            15.550             14.155 
[1] "1.4 - 27.8 (15.6)" "0.1 - 84.1 (14.2)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  11P GAIN MUTATED         0        0        0         5         8         0
  11P GAIN WILD-TYPE       1        6       13        21       109         5
                    vv
clus                 STAGE IV
  11P GAIN MUTATED          0
  11P GAIN WILD-TYPE        4
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                5                 21
  STAGE IIB                8                109
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED     0   0  13   0
  11P GAIN WILD-TYPE   8  21 126   4
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                0                  8
  T2                0                 21
  T3               13                126
  T4                0                  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"
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5   8
  11P GAIN WILD-TYPE  40 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    8
  11P GAIN WILD-TYPE   40  116
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                5                 40
  1                8                116
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    8  0
  11P GAIN WILD-TYPE 72  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    0
  11P GAIN WILD-TYPE   72    4
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                8                 72
  1                0                  4
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2 11
  11P GAIN WILD-TYPE 76 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   11
  11P GAIN WILD-TYPE   76   84
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 76
  MALE                 11                 84
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11P GAIN MUTATED                                    12
  11P GAIN WILD-TYPE                                 133
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11P GAIN MUTATED                                       0
  11P GAIN WILD-TYPE                                    22
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  11P GAIN MUTATED                                                  1
  11P GAIN WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  11P GAIN MUTATED                                     0
  11P GAIN WILD-TYPE                                   1
D21V8, multiclass
                                                  clus
vv                                                 11P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 11P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             133
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            22
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D21V9, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 52 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABI         TCGA-2J-AABO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-2J-AABV         TCGA-2L-AAQA         TCGA-2L-AAQE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-3A-A9I9         TCGA-3A-A9IB         TCGA-3A-A9IJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-6880         TCGA-F2-A8YN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H6-A45N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7886 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8126 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A7M4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-AAUU         TCGA-IB-AAUV         TCGA-LB-A7SX 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-XD-AAUL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"11P GAIN WILD-TYPE" 
D21V10, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 43 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-2J-AABI         TCGA-2J-AABO         TCGA-3A-A9IB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-3A-A9IJ         TCGA-3A-A9IR         TCGA-3A-A9IX 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H8-A6C1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7891 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-A5SS         TCGA-IB-A6UF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUV         TCGA-LB-A7SX 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUI         TCGA-XD-AAUL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"11P GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED     4   8   0   0
  11P GAIN WILD-TYPE 104  43   2   4
D21V11, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                4                104
  R1                8                 43
  R2                0                  2
  RX                0                  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"
D21V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0    12
  11P GAIN WILD-TYPE     3                         7   146
D21V13, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   12                146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0   9
  11P GAIN WILD-TYPE   3 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    9
  11P GAIN WILD-TYPE    3  126
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                9                126
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    3 11
  11Q GAIN WILD-TYPE 76 81
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                157 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                 81 
$`11Q GAIN MUTATED`
TCGA-2J-AAB6 TCGA-3A-A9IZ TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPZ TCGA-FB-AAQ0 
        9.63        10.13         3.12        24.07        23.54        15.55 
TCGA-FB-AAQ1 TCGA-IB-7647 TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-A5SP TCGA-IB-A6UG 
        4.04        21.90         4.04         3.85        15.85         1.35 
TCGA-IB-A7LX TCGA-M8-A5N4 
        8.22        19.20 

$`11Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.72        22.26        31.86        15.91        14.47        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
        3.39        12.95         9.60        45.47        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        30.64        15.06        31.79 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       34.09        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 
       19.46         7.10         7.66        19.27        17.00         5.88 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       14.76        12.43        11.61        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       12.53        34.82         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 
        2.01         5.10        36.20        20.35        15.78        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       12.89        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
        7.76         0.13         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       14.93        17.92         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       12.95        49.38         4.77        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       15.65        41.33         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ 
       21.30        15.98         2.47        17.16        12.00         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       15.12        20.88        21.90        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        8.05        13.28         7.56         9.14        12.92        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       10.29         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        9.40         0.30        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       27.75        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.35               0.13 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             24.07              84.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              9.88              14.40 
[1] "1.4 - 24.1 (9.9)"  "0.1 - 84.1 (14.4)"
[1] "hr=" "2.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  11Q GAIN MUTATED         0        0        0         5        10         0
  11Q GAIN WILD-TYPE       1        6       13        21       107         5
                    vv
clus                 STAGE IV
  11Q GAIN MUTATED          0
  11Q GAIN WILD-TYPE        4
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                5                 21
  STAGE IIB               10                107
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED     0   1  14   0
  11Q GAIN WILD-TYPE   8  20 125   4
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                0                  8
  T2                1                 20
  T3               14                125
  T4                0                  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"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     5  10
  11Q GAIN WILD-TYPE  40 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5   10
  11Q GAIN WILD-TYPE   40  114
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                5                 40
  1               10                114
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    9  0
  11Q GAIN WILD-TYPE 71  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      9    0
  11Q GAIN WILD-TYPE   71    4
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                9                 71
  1                0                  4
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3 12
  11Q GAIN WILD-TYPE 75 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   12
  11Q GAIN WILD-TYPE   75   83
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 75
  MALE                 12                 83
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11Q GAIN MUTATED                                    15
  11Q GAIN WILD-TYPE                                 130
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11Q GAIN MUTATED                                       0
  11Q GAIN WILD-TYPE                                    22
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  11Q GAIN MUTATED                                                  0
  11Q GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  11Q GAIN MUTATED                                     0
  11Q GAIN WILD-TYPE                                   1
D22V8, multiclass
                                                  clus
vv                                                 11Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 11Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             130
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            22
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D22V9, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 52 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABI         TCGA-2J-AABO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-2J-AABV         TCGA-2L-AAQA         TCGA-2L-AAQE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-3A-A9I9         TCGA-3A-A9IB         TCGA-3A-A9IJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-6880         TCGA-F2-A8YN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H6-A45N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7887 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A7M4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-AAUU         TCGA-IB-AAUV         TCGA-LB-A7SX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-XD-AAUL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"11Q GAIN WILD-TYPE" 
D22V10, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 43 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-2J-AABI         TCGA-2J-AABO         TCGA-3A-A9IB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-3A-A9IJ         TCGA-3A-A9IR         TCGA-3A-A9IX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H8-A6C1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7891         TCGA-IB-8126 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUV         TCGA-LB-A7SX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUI         TCGA-XD-AAUL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"11Q GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED     6   8   0   0
  11Q GAIN WILD-TYPE 102  43   2   4
D22V11, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                6                102
  R1                8                 43
  R2                0                  2
  RX                0                  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"
D22V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0    14
  11Q GAIN WILD-TYPE     3                         7   144
D22V13, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   14                144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     2   9
  11Q GAIN WILD-TYPE   1 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    9
  11Q GAIN WILD-TYPE    1  126
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO                9                126
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   12 16
  12P GAIN WILD-TYPE 67 76
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                143 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                16                 76 
$`12P GAIN MUTATED`
TCGA-2J-AABF TCGA-2J-AABI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IB 
       22.72        31.86         9.60        45.47        53.00         7.36 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IV TCGA-F2-A7TX 
       84.10        68.52        63.85        30.64        31.79         3.12 
TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5924 
       15.95        23.54        15.55         4.04         5.03        15.78 
TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-HZ-A77O TCGA-IB-7646 TCGA-IB-7890 
       21.73         0.13         3.95         5.26         4.77        19.66 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-Q3-AA2A TCGA-YH-A8SY 
        1.35         8.22         3.12        12.76 

$`12P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABR 
       22.22        22.26        15.91        14.47        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       12.95        23.61        20.84        24.26        28.73        60.95 
TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       50.70        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
       19.27        17.00         5.88        24.07        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ3 
       11.61        37.15         7.50        12.53        34.82         1.02 
TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        8.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 
       17.79        12.89        13.84        22.06         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
        7.76         0.26        27.62        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
       10.85         1.08         0.23        12.95        49.38        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       15.35        19.82        23.80        15.65        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
        3.62        43.79        15.81        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88        21.90        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
       13.28         7.56         9.14        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M 
       19.20         8.78        15.45        13.68        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        66.28         0.69 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.13               0.23 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             84.10              75.12 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            15.665             14.140 
[1] "0.1 - 84.1 (15.7)" "0.2 - 75.1 (14.1)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  12P GAIN MUTATED         1        1        5         2        17         1
  12P GAIN WILD-TYPE       0        5        8        24       100         4
                    vv
clus                 STAGE IV
  12P GAIN MUTATED          0
  12P GAIN WILD-TYPE        4
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 1                  5
  STAGE IB                 5                  8
  STAGE IIA                2                 24
  STAGE IIB               17                100
  STAGE III                1                  4
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED     2   6  19   0
  12P GAIN WILD-TYPE   6  15 120   4
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                2                  6
  T2                6                 15
  T3               19                120
  T4                0                  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"
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     6  19
  12P GAIN WILD-TYPE  39 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6   19
  12P GAIN WILD-TYPE   39  105
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                6                 39
  1               19                105
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    7  0
  12P GAIN WILD-TYPE 73  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7    0
  12P GAIN WILD-TYPE   73    4
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                7                 73
  1                0                  4
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   10 18
  12P GAIN WILD-TYPE 68 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10   18
  12P GAIN WILD-TYPE   68   77
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               10                 68
  MALE                 18                 77
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12P GAIN MUTATED                                    19
  12P GAIN WILD-TYPE                                 126
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12P GAIN MUTATED                                       8
  12P GAIN WILD-TYPE                                    14
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  12P GAIN MUTATED                                                  0
  12P GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  12P GAIN MUTATED                                     0
  12P GAIN WILD-TYPE                                   1
D23V8, multiclass
                                                  clus
vv                                                 12P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 12P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D23V9, continuous
D23V10, continuous
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED   15  9  0  3
  12P GAIN WILD-TYPE 93 42  2  1
D23V11, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               15                 93
  R1                9                 42
  R2                0                  2
  RX                3                  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"
D23V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       0                         0    27
  12P GAIN WILD-TYPE     3                         7   131
D23V13, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   27                131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  22
  12P GAIN WILD-TYPE   3 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   22
  12P GAIN WILD-TYPE    3  113
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               22                113
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   10 11
  12Q GAIN WILD-TYPE 69 81
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                150 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                 81 
$`12Q GAIN MUTATED`
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IB TCGA-3A-A9IL TCGA-3A-A9IN 
        9.60        45.47        53.00         7.36        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-AAPP TCGA-FB-AAPZ 
       63.85        30.64        31.79         3.12        15.95        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-IB-7646 
       15.55         4.04        21.73         0.13         3.95         4.77 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-Q3-AA2A 
        1.35         8.22         3.12 

$`12Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       22.49         3.39        12.95        23.61        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       28.73        60.95        50.70        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       12.39        75.12        71.74        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.10         7.66        19.27        17.00         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       14.76        12.43        11.61        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
       34.82         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 
        5.10        36.20        20.35        15.78        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       13.84        22.06         0.92        19.50         7.76         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 
        1.08         0.23        12.95        49.38        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       19.82        23.80        15.65        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88        21.90        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
       13.28         7.56         9.14        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M 
       19.20         8.78        15.45        13.68        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.13               0.23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             84.10              75.12 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            15.550             14.155 
[1] "0.1 - 84.1 (15.6)" "0.2 - 75.1 (14.2)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  12Q GAIN MUTATED         1        1        4         1        13         0
  12Q GAIN WILD-TYPE       0        5        9        25       104         5
                    vv
clus                 STAGE IV
  12Q GAIN MUTATED          0
  12Q GAIN WILD-TYPE        4
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 1                  5
  STAGE IB                 4                  9
  STAGE IIA                1                 25
  STAGE IIB               13                104
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED     2   4  14   0
  12Q GAIN WILD-TYPE   6  17 125   4
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                2                  6
  T2                4                 17
  T3               14                125
  T4                0                  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"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4  14
  12Q GAIN WILD-TYPE  41 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4   14
  12Q GAIN WILD-TYPE   41  110
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                4                 41
  1               14                110
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    3  0
  12Q GAIN WILD-TYPE 77  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    0
  12Q GAIN WILD-TYPE   77    4
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                3                 77
  1                0                  4
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    6 15
  12Q GAIN WILD-TYPE 72 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      6   15
  12Q GAIN WILD-TYPE   72   80
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                6                 72
  MALE                 15                 80
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12Q GAIN MUTATED                                    14
  12Q GAIN WILD-TYPE                                 131
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12Q GAIN MUTATED                                       7
  12Q GAIN WILD-TYPE                                    15
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  12Q GAIN MUTATED                                                  0
  12Q GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  12Q GAIN MUTATED                                     0
  12Q GAIN WILD-TYPE                                   1
D24V8, multiclass
                                                  clus
vv                                                 12Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            14
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 12Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             131
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D24V9, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 52 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABI         TCGA-2J-AABO 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-2J-AABV         TCGA-2L-AAQA         TCGA-2L-AAQE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-3A-A9I9         TCGA-3A-A9IJ         TCGA-3A-A9IX 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F2-6880         TCGA-F2-A8YN         TCGA-FB-A4P5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-A7DR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-FB-AAPY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-H6-8124         TCGA-H6-A45N         TCGA-H8-A6C1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A7M4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-AAUU         TCGA-IB-AAUV         TCGA-LB-A7SX 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-XD-AAUL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"12Q GAIN WILD-TYPE" 
D24V10, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 43 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-2J-AABI         TCGA-2J-AABO         TCGA-3A-A9IJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-3A-A9IR         TCGA-3A-A9IX         TCGA-FB-A4P5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-A7DR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-FB-AAPY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-H6-8124         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7891         TCGA-IB-8126 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUV         TCGA-LB-A7SX 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUI         TCGA-XD-AAUL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"12Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN MUTATED   11  7  0  3
  12Q GAIN WILD-TYPE 97 44  2  1
D24V11, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               11                 97
  R1                7                 44
  R2                0                  2
  RX                3                  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"
D24V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       0                         0    21
  12Q GAIN WILD-TYPE     3                         7   137
D24V13, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   21                137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  18
  12Q GAIN WILD-TYPE   3 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   18
  12Q GAIN WILD-TYPE    3  117
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               18                117
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   14 12
  13Q GAIN WILD-TYPE 65 80
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                26                145 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                12                 80 
$`13Q GAIN MUTATED`
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABP TCGA-2J-AABT 
        9.63         2.63        22.72        22.26        11.84        10.49 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IV TCGA-3A-A9J0 
        9.60        45.47        84.10        63.85        31.79        12.39 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ6 TCGA-FZ-5921 TCGA-H6-A45N 
       23.54        15.55         5.03         8.02         5.10        13.84 
TCGA-HZ-7922 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7645 TCGA-IB-A5SO TCGA-IB-A7LX 
        0.13         5.26        10.85        49.38        12.00         8.22 
TCGA-IB-AAUU TCGA-YB-A89D 
        8.05        11.51 

$`13Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABI 
        2.17        23.97        20.61        19.96        22.22        31.86 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.91        14.47        14.40         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       22.49         3.39        12.95        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IR 
        7.36        24.26        28.73        60.95        68.52        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       30.64        15.06        34.09        10.13        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.70        19.46         7.10         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
        3.12        17.00         5.88        24.07        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.61        15.95        37.15         7.50        12.53        34.82 
TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 
        4.04         1.02        24.36         2.01        36.20        20.35 
TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
       15.78        17.79        12.89        22.06        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
       19.50         7.76         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       14.93        17.92         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 
        6.38        21.60         1.08         0.23        12.95         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       21.90        15.35        19.82        23.80        15.65        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SQ 
        3.85        15.98         2.47        17.16        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.12        20.88        21.90         1.35        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        9.44        13.28         7.56         9.14        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        27.75        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH 
       13.81        12.99        12.03        13.32        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.13               0.23 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             84.10              75.12 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            11.675             14.930 
[1] "0.1 - 84.1 (11.7)" "0.2 - 75.1 (14.9)"
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  13Q GAIN MUTATED         1        1        1         3        19         0
  13Q GAIN WILD-TYPE       0        5       12        23        98         5
                    vv
clus                 STAGE IV
  13Q GAIN MUTATED          0
  13Q GAIN WILD-TYPE        4
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 1                  5
  STAGE IB                 1                 12
  STAGE IIA                3                 23
  STAGE IIB               19                 98
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED     2   3  20   0
  13Q GAIN WILD-TYPE   6  18 119   4
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                2                  6
  T2                3                 18
  T3               20                119
  T4                0                  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"
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5  19
  13Q GAIN WILD-TYPE  40 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   19
  13Q GAIN WILD-TYPE   40  105
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                5                 40
  1               19                105
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   10  0
  13Q GAIN WILD-TYPE 70  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     10    0
  13Q GAIN WILD-TYPE   70    4
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               10                 70
  1                0                  4
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   10 16
  13Q GAIN WILD-TYPE 68 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     10   16
  13Q GAIN WILD-TYPE   68   79
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               10                 68
  MALE                 16                 79
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  13Q GAIN MUTATED                                    18
  13Q GAIN WILD-TYPE                                 127
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  13Q GAIN MUTATED                                       7
  13Q GAIN WILD-TYPE                                    15
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  13Q GAIN MUTATED                                                  0
  13Q GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  13Q GAIN MUTATED                                     1
  13Q GAIN WILD-TYPE                                   0
D25V8, multiclass
                                                  clus
vv                                                 13Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 13Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D25V9, continuous
D25V10, continuous
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 44 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABI 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-3A-A9IR         TCGA-3A-A9IX         TCGA-FB-A4P5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-A7DR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-FB-AAPY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-H6-8124         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7891         TCGA-IB-8126 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-IB-AAUV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-US-A774         TCGA-XD-AAUI 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-YY-A8LH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED   19  4  0  1
  13Q GAIN WILD-TYPE 89 47  2  3
D25V11, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               19                 89
  R1                4                 47
  R2                0                  2
  RX                1                  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"
D25V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         0    24
  13Q GAIN WILD-TYPE     3                         7   134
D25V13, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   24                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  15
  13Q GAIN WILD-TYPE   3 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   15
  13Q GAIN WILD-TYPE    3  120
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               15                120
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   14 10
  14Q GAIN WILD-TYPE 65 82
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                24                147 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                10                 82 
$`14Q GAIN MUTATED`
TCGA-2J-AAB6 TCGA-2J-AABO TCGA-2L-AAQM TCGA-3A-A9IB TCGA-3A-A9IN TCGA-3A-A9IO 
        9.63        14.47        45.47         7.36        68.52        63.85 
TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-FB-AAQ6 
       31.79         3.12        24.07        15.95        23.54         8.02 
TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A6UG 
        0.13        17.92         6.38         4.04        17.16         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUU TCGA-M8-A5N4 TCGA-S4-A8RO TCGA-YB-A89D 
        8.22        15.88         8.05        19.20        17.26        11.51 

$`14Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR 
       22.72        22.26        31.86        15.91        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        53.00        23.61        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       28.73        60.95        84.10        50.70        30.64        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN 
        9.70        19.46         7.10         7.66        19.27        17.00 
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS 
        5.88        14.76        12.43        11.61        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        34.82        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 
       24.36         2.01         5.10        36.20        20.35        15.78 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
       17.79        12.89        13.84        22.06        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
       19.50         7.76         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK 
       14.93         4.96        21.70        16.14        10.13        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        4.77        21.90        15.35        19.82        23.80        15.65 
TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       41.33         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
        3.85        15.98         2.47        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       15.12        20.88        21.90         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         9.44        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.56         9.14        12.92        12.46        10.29         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       15.45        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       21.24        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.13               0.23 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             68.52              84.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            15.175             14.140 
[1] "0.1 - 68.5 (15.2)" "0.2 - 84.1 (14.1)"
[1] "hr=" "1.4"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  14Q GAIN MUTATED         0        1        2         2        18         0
  14Q GAIN WILD-TYPE       1        5       11        24        99         5
                    vv
clus                 STAGE IV
  14Q GAIN MUTATED          1
  14Q GAIN WILD-TYPE        3
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  5
  STAGE IB                 2                 11
  STAGE IIA                2                 24
  STAGE IIB               18                 99
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED     1   3  20   0
  14Q GAIN WILD-TYPE   7  18 119   4
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                  7
  T2                3                 18
  T3               20                119
  T4                0                  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"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  18
  14Q GAIN WILD-TYPE  40 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   18
  14Q GAIN WILD-TYPE   40  106
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                5                 40
  1               18                106
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    9  1
  14Q GAIN WILD-TYPE 71  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9    1
  14Q GAIN WILD-TYPE   71    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                9                 71
  1                1                  3
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    9 16
  14Q GAIN WILD-TYPE 69 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9   16
  14Q GAIN WILD-TYPE   69   79
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                9                 69
  MALE                 16                 79
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  14Q GAIN MUTATED                                    21
  14Q GAIN WILD-TYPE                                 124
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  14Q GAIN MUTATED                                       4
  14Q GAIN WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  14Q GAIN MUTATED                                                  0
  14Q GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  14Q GAIN MUTATED                                     0
  14Q GAIN WILD-TYPE                                   1
D26V8, multiclass
                                                  clus
vv                                                 14Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 14Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D26V9, continuous
D26V10, continuous
                    vv
clus                 R0 R1 R2 RX
  14Q GAIN MUTATED   14 10  0  0
  14Q GAIN WILD-TYPE 94 41  2  4
D26V11, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               14                 94
  R1               10                 41
  R2                0                  2
  RX                0                  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"
D26V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0    24
  14Q GAIN WILD-TYPE     3                         7   134
D26V13, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   24                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  18
  14Q GAIN WILD-TYPE   2 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   18
  14Q GAIN WILD-TYPE    2  117
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               18                117
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    6  7
  15Q GAIN WILD-TYPE 73 85
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                13                158 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                 85 
$`15Q GAIN MUTATED`
TCGA-2J-AABO TCGA-2L-AAQL TCGA-3A-A9IL TCGA-3A-A9J0 TCGA-F2-A7TX TCGA-FZ-5921 
       14.47         9.60        84.10        12.39         3.12         5.10 
TCGA-HZ-7922 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-AAUU TCGA-RB-A7B8 TCGA-S4-A8RP 
        0.13         4.04        15.81         8.05        15.32        23.08 
TCGA-US-A776 
       27.75 

$`15Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABP 
       22.22        22.72        22.26        31.86        15.91        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95        45.47        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        24.26        28.73        60.95        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        30.64        15.06        31.79        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
        7.66        19.27        17.00         5.88        24.07        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       12.43        11.61        15.95        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       34.82        23.54        15.55         4.04         5.03         1.02 
TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 
        8.02        24.36         2.01        36.20        20.35        15.78 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
       17.79        12.89        13.84        22.06        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
       19.50         7.76         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       14.93        17.92         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       12.95        49.38         4.77        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 
       23.80        15.65        41.33         3.62        43.79        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         9.44        13.28         7.56 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        9.14        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       15.45        13.68         3.12         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       17.26        22.85        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.13               0.23 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             84.10              75.12 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            12.390             14.285 
[1] "0.1 - 84.1 (12.4)" "0.2 - 75.1 (14.3)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  15Q GAIN MUTATED         1        0        0         1        11         0
  15Q GAIN WILD-TYPE       0        6       13        25       106         5
                    vv
clus                 STAGE IV
  15Q GAIN MUTATED          0
  15Q GAIN WILD-TYPE        4
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                1                 25
  STAGE IIB               11                106
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED     1   0  12   0
  15Q GAIN WILD-TYPE   7  21 127   4
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                1                  7
  T2                0                 21
  T3               12                127
  T4                0                  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"
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  11
  15Q GAIN WILD-TYPE  44 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   11
  15Q GAIN WILD-TYPE   44  113
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                1                 44
  1               11                113
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6  0
  15Q GAIN WILD-TYPE 74  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6    0
  15Q GAIN WILD-TYPE   74    4
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                6                 74
  1                0                  4
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6  7
  15Q GAIN WILD-TYPE 72 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6    7
  15Q GAIN WILD-TYPE   72   88
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                6                 72
  MALE                  7                 88
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  15Q GAIN MUTATED                                    10
  15Q GAIN WILD-TYPE                                 135
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  15Q GAIN MUTATED                                       2
  15Q GAIN WILD-TYPE                                    20
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  15Q GAIN MUTATED                                                  1
  15Q GAIN WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  15Q GAIN MUTATED                                     0
  15Q GAIN WILD-TYPE                                   1
D27V8, multiclass
                                                  clus
vv                                                 15Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 15Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             135
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            20
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D27V9, continuous
D27V10, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 43 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2J-AABI         TCGA-3A-A9IB         TCGA-3A-A9IJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-3A-A9IR         TCGA-3A-A9IX         TCGA-FB-A4P5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-A7DR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-FB-AAPY 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-H6-8124         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A6UG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUV         TCGA-LB-A7SX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUI         TCGA-XD-AAUL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"15Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  15Q GAIN MUTATED    9  2  0  1
  15Q GAIN WILD-TYPE 99 49  2  3
D27V11, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                9                 99
  R1                2                 49
  R2                0                  2
  RX                1                  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"
D27V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         0    12
  15Q GAIN WILD-TYPE     3                         7   146
D27V13, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   12                146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0   8
  15Q GAIN WILD-TYPE   3 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    8
  15Q GAIN WILD-TYPE    3  127
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                8                127
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    8 14
  16P GAIN WILD-TYPE 71 78
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                149 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                14                 78 
$`16P GAIN MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2L-AAQL TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9J0 
        2.63        22.72         9.60         7.36        24.26        12.39 
TCGA-FB-AAPP TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-HZ-7289 TCGA-HZ-8636 TCGA-HZ-A77O 
       15.95        15.55         4.04        21.73        17.92         5.26 
TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7890 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7M4 
       15.65         4.04        19.66        17.16        15.85        15.88 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-YB-A89D 
        8.05        12.92        19.20        11.51 

$`16P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABR 
       22.26        31.86        15.91        14.47        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IH 
       12.95        45.47        53.00        23.61        20.84        28.73 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        84.10        68.52        63.85        50.70        30.64 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        31.79        34.09        10.13        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.70        19.46         7.10         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
        3.12        17.00         5.88        24.07        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       11.61        37.15         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        5.03         1.02         8.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       22.06         0.92        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q 
       16.14        10.13         6.38        21.60        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        0.23        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       19.82        23.80        41.33         3.62        43.79        15.81 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ 
       21.30         3.85        15.98         2.47        12.00         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM 
       15.12        20.88        21.90         1.35         8.22         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 
        9.44        13.28         7.56         9.14        12.46        10.29 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        12.76        66.28         0.69 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              2.63               0.13 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             24.26              84.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             15.60              14.14 
[1] "2.6 - 24.3 (15.6)" "0.1 - 84.1 (14.1)"
[1] "hr=" "1.5"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  16P GAIN MUTATED         0        0        1         3        17         0
  16P GAIN WILD-TYPE       1        6       12        23       100         5
                    vv
clus                 STAGE IV
  16P GAIN MUTATED          1
  16P GAIN WILD-TYPE        3
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 1                 12
  STAGE IIA                3                 23
  STAGE IIB               17                100
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED     0   3  19   0
  16P GAIN WILD-TYPE   8  18 120   4
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                0                  8
  T2                3                 18
  T3               19                120
  T4                0                  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"
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     5  17
  16P GAIN WILD-TYPE  40 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   17
  16P GAIN WILD-TYPE   40  107
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                5                 40
  1               17                107
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    9  1
  16P GAIN WILD-TYPE 71  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    1
  16P GAIN WILD-TYPE   71    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                9                 71
  1                1                  3
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    6 16
  16P GAIN WILD-TYPE 72 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6   16
  16P GAIN WILD-TYPE   72   79
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                6                 72
  MALE                 16                 79
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16P GAIN MUTATED                                    21
  16P GAIN WILD-TYPE                                 124
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16P GAIN MUTATED                                       1
  16P GAIN WILD-TYPE                                    21
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  16P GAIN MUTATED                                                  0
  16P GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  16P GAIN MUTATED                                     0
  16P GAIN WILD-TYPE                                   1
D28V8, multiclass
                                                  clus
vv                                                 16P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 16P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D28V9, continuous
D28V10, continuous
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED   11  9  0  2
  16P GAIN WILD-TYPE 97 42  2  2
D28V11, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               11                 97
  R1                9                 42
  R2                0                  2
  RX                2                  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"
D28V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       0                         1    19
  16P GAIN WILD-TYPE     3                         6   139
D28V13, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   19                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  16
  16P GAIN WILD-TYPE   3 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   16
  16P GAIN WILD-TYPE    3  119
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               16                119
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   10 12
  16Q GAIN WILD-TYPE 69 80
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                22                149 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                12                 80 
$`16Q GAIN MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABF TCGA-3A-A9IB TCGA-3A-A9J0 TCGA-FB-A545 TCGA-FB-AAPP 
        2.63        22.72         7.36        12.39        24.07        15.95 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-HZ-A77O 
       23.54        15.55         4.04        17.92        21.60         5.26 
TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7890 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7M4 
       15.65         4.04        19.66        17.16        15.85        15.88 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-YB-A89D 
        8.05        12.92        19.20        11.51 

$`16Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABR 
       22.26        31.86        15.91        14.47        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       12.95         9.60        45.47        53.00        23.61        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        28.73        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        30.64        15.06        31.79        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM 
        7.66        19.27         3.12        17.00         5.88        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       12.43        11.61        37.15         7.50        12.53        34.82 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        5.03         1.02         8.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       22.06        21.73         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
        0.69         3.95         9.83        12.43        14.93         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-HZ-A77Q 
       21.70        16.14        10.13         6.38        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        0.23        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       19.82        23.80        41.33         3.62        43.79        15.81 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ 
       21.30         3.85        15.98         2.47        12.00         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM 
       15.12        20.88        21.90         1.35         8.22         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 
        9.44        13.28         7.56         9.14        12.46        10.29 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        12.76        66.28         0.69 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              2.63               0.13 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             24.07              84.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             15.75              13.84 
[1] "2.6 - 24.1 (15.8)" "0.1 - 84.1 (13.8)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  16Q GAIN MUTATED         0        0        1         3        17         0
  16Q GAIN WILD-TYPE       1        6       12        23       100         5
                    vv
clus                 STAGE IV
  16Q GAIN MUTATED          1
  16Q GAIN WILD-TYPE        3
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 1                 12
  STAGE IIA                3                 23
  STAGE IIB               17                100
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED     0   4  18   0
  16Q GAIN WILD-TYPE   8  17 121   4
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                0                  8
  T2                4                 17
  T3               18                121
  T4                0                  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"
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5  17
  16Q GAIN WILD-TYPE  40 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   17
  16Q GAIN WILD-TYPE   40  107
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                5                 40
  1               17                107
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   10  1
  16Q GAIN WILD-TYPE 70  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    1
  16Q GAIN WILD-TYPE   70    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               10                 70
  1                1                  3
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    6 16
  16Q GAIN WILD-TYPE 72 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6   16
  16Q GAIN WILD-TYPE   72   79
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                6                 72
  MALE                 16                 79
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16Q GAIN MUTATED                                    21
  16Q GAIN WILD-TYPE                                 124
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16Q GAIN MUTATED                                       1
  16Q GAIN WILD-TYPE                                    21
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  16Q GAIN MUTATED                                                  0
  16Q GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  16Q GAIN MUTATED                                     0
  16Q GAIN WILD-TYPE                                   1
D29V8, multiclass
                                                  clus
vv                                                 16Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 16Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D29V9, continuous
D29V10, continuous
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED   11 10  0  0
  16Q GAIN WILD-TYPE 97 41  2  4
D29V11, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               11                 97
  R1               10                 41
  R2                0                  2
  RX                0                  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"
D29V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         1    19
  16Q GAIN WILD-TYPE     3                         6   139
D29V13, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   19                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  17
  16Q GAIN WILD-TYPE   3 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   17
  16Q GAIN WILD-TYPE    3  118
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               17                118
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    8  1
  17P GAIN WILD-TYPE 71 91
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                162 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 91 
$`17P GAIN MUTATED`
TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       11.84        45.47        53.00        84.10        68.52        63.85 
TCGA-3A-A9IV TCGA-IB-7646 TCGA-LB-A8F3 
       31.79         4.77        12.46 

$`17P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39        12.95         9.60        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        28.73        60.95        50.70        30.64        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.70        19.46         7.10         7.66        19.27         3.12 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR 
       17.00         5.88        24.07        14.76        12.43        11.61 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       15.95        37.15         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       15.55         4.04         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 
        2.01         5.10        36.20        20.35        15.78        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       12.89        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
        7.76         0.13         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       14.93        17.92         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       12.95        49.38        21.90        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       15.65        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 
       13.28         7.56         9.14        12.92        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              4.77               0.13 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             84.10              75.12 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             45.47              13.99 
[1] "4.8 - 84.1 (45.5)" "0.1 - 75.1 (14.0)"
[1] "hr=" "12" 
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  17P GAIN MUTATED         1        1        2         1         3         0
  17P GAIN WILD-TYPE       0        5       11        25       114         5
                    vv
clus                 STAGE IV
  17P GAIN MUTATED          0
  17P GAIN WILD-TYPE        4
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 1                  5
  STAGE IB                 2                 11
  STAGE IIA                1                 25
  STAGE IIB                3                114
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED     2   2   4   0
  17P GAIN WILD-TYPE   6  19 135   4
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                2                  6
  T2                2                 19
  T3                4                135
  T4                0                  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"
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     3   3
  17P GAIN WILD-TYPE  42 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    3
  17P GAIN WILD-TYPE   42  121
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                3                 42
  1                3                121
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    2  0
  17P GAIN WILD-TYPE 78  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    0
  17P GAIN WILD-TYPE   78    4
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                2                 78
  1                0                  4
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  4
  17P GAIN WILD-TYPE 73 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    4
  17P GAIN WILD-TYPE   73   91
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                5                 73
  MALE                  4                 91
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17P GAIN MUTATED                                     3
  17P GAIN WILD-TYPE                                 142
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17P GAIN MUTATED                                       5
  17P GAIN WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  17P GAIN MUTATED                                                  0
  17P GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  17P GAIN MUTATED                                     1
  17P GAIN WILD-TYPE                                   0
D30V8, multiclass
                                                  clus
vv                                                 17P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 17P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             142
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D30V9, continuous
D30V10, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     6   3   0   0
  17P GAIN WILD-TYPE 102  48   2   4
D30V11, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                6                102
  R1                3                 48
  R2                0                  2
  RX                0                  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"
D30V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       0                         1     8
  17P GAIN WILD-TYPE     3                         6   150
D30V13, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    8                150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0   7
  17P GAIN WILD-TYPE   3 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    7
  17P GAIN WILD-TYPE    3  128
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                7                128
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   13  3
  17Q GAIN WILD-TYPE 66 89
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                155 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 89 
$`17Q GAIN MUTATED`
TCGA-2J-AABI TCGA-2J-AABO TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-3A-A9IN 
       31.86        14.47        45.47        53.00        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IV TCGA-FB-A545 TCGA-FB-AAQ1 TCGA-HZ-7922 TCGA-IB-7646 
       63.85        31.79        24.07         4.04         0.13         4.77 
TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-S4-A8RO 
       15.88        12.46        19.20        17.26 

$`17Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       28.73        60.95        50.70        30.64        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ 
        5.88        14.76        12.43        11.61        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 
        7.50        12.53        34.82        23.54        15.55         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       20.35        15.78        17.79        12.89        13.84        22.06 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 
       21.73         0.92        19.50         7.76         0.26        27.62 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       20.19        17.03        23.21        12.03         0.69         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 
        1.08         0.23        12.95        49.38        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       19.82        23.80        15.65        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         1.35         8.22         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A9Q5 
        8.05        13.28         7.56         9.14        12.92        10.29 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
        0.30        21.24        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       14.14         0.39        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.13               0.23 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             84.10              75.12 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            21.635             13.680 
[1] "0.1 - 84.1 (21.6)" "0.2 - 75.1 (13.7)"
[1] "hr=" "5.4"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  17Q GAIN MUTATED         1        1        2         3         8         0
  17Q GAIN WILD-TYPE       0        5       11        23       109         5
                    vv
clus                 STAGE IV
  17Q GAIN MUTATED          0
  17Q GAIN WILD-TYPE        4
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 1                  5
  STAGE IB                 2                 11
  STAGE IIA                3                 23
  STAGE IIB                8                109
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED     2   2  11   0
  17Q GAIN WILD-TYPE   6  19 128   4
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                2                  6
  T2                2                 19
  T3               11                128
  T4                0                  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"
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     5   8
  17Q GAIN WILD-TYPE  40 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    8
  17Q GAIN WILD-TYPE   40  116
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                5                 40
  1                8                116
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    5  0
  17Q GAIN WILD-TYPE 75  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    0
  17Q GAIN WILD-TYPE   75    4
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                5                 75
  1                0                  4
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    9  7
  17Q GAIN WILD-TYPE 69 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      9    7
  17Q GAIN WILD-TYPE   69   88
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                9                 69
  MALE                  7                 88
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17Q GAIN MUTATED                                    10
  17Q GAIN WILD-TYPE                                 135
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17Q GAIN MUTATED                                       6
  17Q GAIN WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  17Q GAIN MUTATED                                                  0
  17Q GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  17Q GAIN MUTATED                                     0
  17Q GAIN WILD-TYPE                                   1
D31V8, multiclass
                                                  clus
vv                                                 17Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 17Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             135
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D31V9, continuous
D31V10, continuous
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED    9  6  0  0
  17Q GAIN WILD-TYPE 99 45  2  4
D31V11, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                9                 99
  R1                6                 45
  R2                0                  2
  RX                0                  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"
D31V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         1    14
  17Q GAIN WILD-TYPE     3                         6   144
D31V13, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   14                144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  12
  17Q GAIN WILD-TYPE   3 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   12
  17Q GAIN WILD-TYPE    3  123
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               12                123
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   12 14
  18P GAIN WILD-TYPE 67 78
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                26                145 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 78 
$`18P GAIN MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQE 
        2.63        22.26        14.47        11.84         9.11        22.49 
TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IV TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-FB-AAQ0 
       45.47        68.52        31.79        15.95        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FZ-5921 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7925 
        4.04         5.10        22.06        21.73        19.50        20.19 
TCGA-HZ-8636 TCGA-HZ-A77O TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A7LX TCGA-IB-A7M4 
       17.92         5.26         3.85        17.16         8.22        15.88 
TCGA-PZ-A5RE TCGA-US-A776 
       15.45        27.75 

$`18P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABV 
       22.72        31.86        15.91        14.40        10.49        21.44 
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
        4.70         3.39        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        30.64        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       12.39        75.12        71.74        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
        7.10         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS 
       24.07        14.76        12.43        11.61        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       12.53        34.82         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 
        2.01        36.20        20.35        15.78        17.79        12.89 
TCGA-H6-A45N TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
       13.84         0.92         7.76         0.13         0.26        27.62 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
        6.38        21.60        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       15.65        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.66        21.30        15.98         2.47        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM 
        7.20        15.12        20.88        21.90         1.35         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX 
        9.44         8.05        13.28         7.56         9.14        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29        19.20         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       22.85        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              2.63               0.13 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             68.52              84.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            16.555             13.320 
[1] "2.6 - 68.5 (16.6)" "0.1 - 84.1 (13.3)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  18P GAIN MUTATED         0        0        2         5        18         0
  18P GAIN WILD-TYPE       1        6       11        21        99         5
                    vv
clus                 STAGE IV
  18P GAIN MUTATED          1
  18P GAIN WILD-TYPE        3
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 2                 11
  STAGE IIA                5                 21
  STAGE IIB               18                 99
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED     0   4  22   0
  18P GAIN WILD-TYPE   8  17 117   4
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                  8
  T2                4                 17
  T3               22                117
  T4                0                  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"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     7  18
  18P GAIN WILD-TYPE  38 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7   18
  18P GAIN WILD-TYPE   38  106
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                7                 38
  1               18                106
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   10  1
  18P GAIN WILD-TYPE 70  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     10    1
  18P GAIN WILD-TYPE   70    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               10                 70
  1                1                  3
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8 18
  18P GAIN WILD-TYPE 70 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8   18
  18P GAIN WILD-TYPE   70   77
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                8                 70
  MALE                 18                 77
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18P GAIN MUTATED                                    18
  18P GAIN WILD-TYPE                                 127
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18P GAIN MUTATED                                       6
  18P GAIN WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  18P GAIN MUTATED                                                  1
  18P GAIN WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  18P GAIN MUTATED                                     1
  18P GAIN WILD-TYPE                                   0
D32V8, multiclass
                                                  clus
vv                                                 18P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 18P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D32V9, continuous
D32V10, continuous
                    vv
clus                 R0 R1 R2 RX
  18P GAIN MUTATED   16  7  0  1
  18P GAIN WILD-TYPE 92 44  2  3
D32V11, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               16                 92
  R1                7                 44
  R2                0                  2
  RX                1                  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"
D32V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         0    25
  18P GAIN WILD-TYPE     3                         7   133
D32V13, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   25                133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  18
  18P GAIN WILD-TYPE   3 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   18
  18P GAIN WILD-TYPE    3  117
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               18                117
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    8  4
  18Q GAIN WILD-TYPE 71 88
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                159 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 88 
$`18Q GAIN MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IV TCGA-FB-AAPP 
        2.63        11.84        45.47        68.52        31.79        15.95 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FZ-5921 TCGA-IB-7886 TCGA-IB-A7M4 TCGA-US-A776 
       23.54         4.04         5.10         4.04        15.88        27.75 

$`18Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.72        22.26        31.86        15.91        14.47        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        53.00        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        28.73        60.95        84.10        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       30.64        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
       19.27         3.12        17.00         5.88        24.07        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       12.43        11.61        37.15         7.50        12.53        34.82 
TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       22.06        21.73         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        4.77        21.90        15.35        19.82        23.80        15.65 
TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       41.33         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       13.68         3.12        15.32         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       17.26        23.08        22.85        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              2.63               0.13 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             68.52              84.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            15.915             14.140 
[1] "2.6 - 68.5 (15.9)" "0.1 - 84.1 (14.1)"
[1] "hr=" "2"  
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  18Q GAIN MUTATED         0        0        2         1         9         0
  18Q GAIN WILD-TYPE       1        6       11        25       108         5
                    vv
clus                 STAGE IV
  18Q GAIN MUTATED          0
  18Q GAIN WILD-TYPE        4
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 2                 11
  STAGE IIA                1                 25
  STAGE IIB                9                108
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED     0   3   9   0
  18Q GAIN WILD-TYPE   8  18 130   4
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                  8
  T2                3                 18
  T3                9                130
  T4                0                  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"
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2   9
  18Q GAIN WILD-TYPE  43 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    9
  18Q GAIN WILD-TYPE   43  115
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                2                 43
  1                9                115
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  0
  18Q GAIN WILD-TYPE 76  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE   76    4
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                4                 76
  1                0                  4
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  8
  18Q GAIN WILD-TYPE 74 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    8
  18Q GAIN WILD-TYPE   74   87
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                 74
  MALE                  8                 87
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18Q GAIN MUTATED                                     7
  18Q GAIN WILD-TYPE                                 138
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18Q GAIN MUTATED                                       3
  18Q GAIN WILD-TYPE                                    19
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  18Q GAIN MUTATED                                                  1
  18Q GAIN WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  18Q GAIN MUTATED                                     1
  18Q GAIN WILD-TYPE                                   0
D33V8, multiclass
                                                  clus
vv                                                 18Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 18Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             138
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D33V9, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 52 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABI         TCGA-2J-AABO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2J-AABV         TCGA-2L-AAQA         TCGA-2L-AAQE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-3A-A9I9         TCGA-3A-A9IB         TCGA-3A-A9IJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-6880         TCGA-F2-A8YN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H6-A45N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7887 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A6UG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-AAUU         TCGA-IB-AAUV         TCGA-LB-A7SX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-XD-AAUL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"18Q GAIN WILD-TYPE" 
D33V10, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 43 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2J-AABI         TCGA-2J-AABO         TCGA-3A-A9IB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-3A-A9IJ         TCGA-3A-A9IR         TCGA-3A-A9IX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H8-A6C1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7891         TCGA-IB-8126 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUV         TCGA-LB-A7SX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUI         TCGA-XD-AAUL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"18Q GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     6   5   0   0
  18Q GAIN WILD-TYPE 102  46   2   4
D33V11, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                6                102
  R1                5                 46
  R2                0                  2
  RX                0                  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"
D33V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0    11
  18Q GAIN WILD-TYPE     3                         7   147
D33V13, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   11                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   8
  18Q GAIN WILD-TYPE   3 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    8
  18Q GAIN WILD-TYPE    3  127
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                8                127
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    9  6
  19P GAIN WILD-TYPE 70 86
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                156 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 86 
$`19P GAIN MUTATED`
TCGA-2J-AAB8 TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IS TCGA-3A-A9IV 
        2.63         9.60        45.47        68.52        30.64        31.79 
TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-IB-7886 TCGA-IB-8127 
        3.12        24.07        34.82        23.54         4.04        17.16 
TCGA-IB-AAUQ TCGA-US-A776 TCGA-YB-A89D 
        6.02        27.75        11.51 

$`19P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.72        22.26        31.86        15.91        14.47        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39        12.95        53.00        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        28.73        60.95        84.10        63.85        50.70 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.70        19.46         7.10         7.66        19.27 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP 
       17.00         5.88        14.76        12.43        11.61        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        12.53        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       20.35        15.78        17.79        12.89        13.84        22.06 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       21.73         0.92        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        3.95         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       21.90        15.35        19.82        23.80        15.65        41.33 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98         2.47        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        4.73         7.86        14.17        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        8.05        13.28         7.56         9.14        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       22.85        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.99        12.03        13.32        12.76        66.28         0.69 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              2.63               0.13 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             68.52              84.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             23.54              13.99 
[1] "2.6 - 68.5 (23.5)" "0.1 - 84.1 (14.0)"
[1] "hr=" "1.9"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  19P GAIN MUTATED         0        0        3         1        11         0
  19P GAIN WILD-TYPE       1        6       10        25       106         5
                    vv
clus                 STAGE IV
  19P GAIN MUTATED          0
  19P GAIN WILD-TYPE        4
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 3                 10
  STAGE IIA                1                 25
  STAGE IIB               11                106
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED     0   5  10   0
  19P GAIN WILD-TYPE   8  16 129   4
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                0                  8
  T2                5                 16
  T3               10                129
  T4                0                  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"
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  11
  19P GAIN WILD-TYPE  42 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   11
  19P GAIN WILD-TYPE   42  113
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                3                 42
  1               11                113
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    6  0
  19P GAIN WILD-TYPE 74  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6    0
  19P GAIN WILD-TYPE   74    4
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                6                 74
  1                0                  4
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    3 12
  19P GAIN WILD-TYPE 75 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   12
  19P GAIN WILD-TYPE   75   83
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                3                 75
  MALE                 12                 83
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19P GAIN MUTATED                                    10
  19P GAIN WILD-TYPE                                 135
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19P GAIN MUTATED                                       4
  19P GAIN WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  19P GAIN MUTATED                                                  1
  19P GAIN WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  19P GAIN MUTATED                                     0
  19P GAIN WILD-TYPE                                   1
D34V8, multiclass
                                                  clus
vv                                                 19P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 19P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             135
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D34V9, continuous
D34V10, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED     6   7   0   1
  19P GAIN WILD-TYPE 102  44   2   3
D34V11, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                6                102
  R1                7                 44
  R2                0                  2
  RX                1                  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"
D34V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         0    15
  19P GAIN WILD-TYPE     3                         7   143
D34V13, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   15                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  11
  19P GAIN WILD-TYPE   3 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   11
  19P GAIN WILD-TYPE    3  124
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               11                124
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   13 10
  19Q GAIN WILD-TYPE 66 82
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                148 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                 82 
$`19Q GAIN MUTATED`
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABH TCGA-2L-AAQL TCGA-2L-AAQM 
        9.63         2.63        22.72        22.26         9.60        45.47 
TCGA-3A-A9IN TCGA-3A-A9IS TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPY 
       68.52        30.64        31.79         3.12        24.07        34.82 
TCGA-FB-AAPZ TCGA-HZ-7922 TCGA-HZ-8001 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8127 
       23.54         0.13        23.21         4.04        21.30        17.16 
TCGA-IB-A6UG TCGA-IB-AAUQ TCGA-LB-A7SX TCGA-US-A776 TCGA-YB-A89D 
        1.35         6.02        12.92        27.75        11.51 

$`19Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABI 
        2.17        23.97        20.61        19.96        22.22        31.86 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU 
       15.91        14.47        11.84        14.40        10.49         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I5 
       21.44         4.70        22.49         3.39        12.95        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       23.61        20.84         7.36        24.26        28.73        60.95 
TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       84.10        63.85        50.70        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       12.39        75.12        71.74        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM 
        7.10         7.66        19.27        17.00         5.88        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       12.43        11.61        15.95        37.15         7.50        12.53 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       15.55         4.04         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 
        2.01         5.10        36.20        20.35        15.78        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       12.89        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8002 
        7.76         0.26        27.62        20.19        17.03        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        4.77        21.90        15.35        19.82        23.80        15.65 
TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7893 
       41.33         3.62        43.79        15.81        19.66         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98         2.47        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
        7.86        14.17        11.11         7.40         9.44         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
       13.28         7.56         9.14        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 
        0.30        21.24        17.26        23.08        22.85        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       14.14         0.39        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        12.76        66.28         0.69 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.13               0.23 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             68.52              84.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             21.30              13.99 
[1] "0.1 - 68.5 (21.3)" "0.2 - 84.1 (14.0)"
[1] "hr=" "1.6"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  19Q GAIN MUTATED         0        0        3         3        16         1
  19Q GAIN WILD-TYPE       1        6       10        23       101         4
                    vv
clus                 STAGE IV
  19Q GAIN MUTATED          0
  19Q GAIN WILD-TYPE        4
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 3                 10
  STAGE IIA                3                 23
  STAGE IIB               16                101
  STAGE III                1                  4
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED     0   5  17   1
  19Q GAIN WILD-TYPE   8  16 122   3
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                0                  8
  T2                5                 16
  T3               17                122
  T4                1                  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"
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     6  16
  19Q GAIN WILD-TYPE  39 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6   16
  19Q GAIN WILD-TYPE   39  108
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                6                 39
  1               16                108
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   11  0
  19Q GAIN WILD-TYPE 69  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     11    0
  19Q GAIN WILD-TYPE   69    4
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               11                 69
  1                0                  4
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    6 17
  19Q GAIN WILD-TYPE 72 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6   17
  19Q GAIN WILD-TYPE   72   78
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                6                 72
  MALE                 17                 78
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19Q GAIN MUTATED                                    17
  19Q GAIN WILD-TYPE                                 128
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19Q GAIN MUTATED                                       5
  19Q GAIN WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  19Q GAIN MUTATED                                                  1
  19Q GAIN WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  19Q GAIN MUTATED                                     0
  19Q GAIN WILD-TYPE                                   1
D35V8, multiclass
                                                  clus
vv                                                 19Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            17
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 19Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D35V9, continuous
D35V10, continuous
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED   11 10  0  1
  19Q GAIN WILD-TYPE 97 41  2  3
D35V11, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               11                 97
  R1               10                 41
  R2                0                  2
  RX                1                  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"
D35V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       0                         1    22
  19Q GAIN WILD-TYPE     3                         6   136
D35V13, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   22                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0  16
  19Q GAIN WILD-TYPE   3 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   16
  19Q GAIN WILD-TYPE    3  119
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               16                119
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   18 15
  20P GAIN WILD-TYPE 61 77
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                33                138 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                15                 77 
$`20P GAIN MUTATED`
TCGA-2J-AABF TCGA-2J-AABP TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IO 
       22.72        11.84         9.60        45.47        68.52        63.85 
TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPP 
       30.64        31.79        12.39        24.07        14.76        15.95 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ6 TCGA-FZ-5921 TCGA-HZ-7289 TCGA-HZ-7922 
       23.54        15.55         8.02         5.10        21.73         0.13 
TCGA-HZ-8005 TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7646 TCGA-IB-7886 TCGA-IB-7890 
        3.95         5.26         1.08         4.77         4.04        19.66 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7LX TCGA-LB-A8F3 TCGA-S4-A8RO TCGA-US-A776 
       17.16        15.85         8.22        12.46        17.26        27.75 
TCGA-US-A77E TCGA-YB-A89D TCGA-YY-A8LH 
       14.14        11.51        66.28 

$`20P GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.26        31.86        15.91        14.47        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95        53.00        23.61        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX 
       28.73        60.95        84.10        50.70        15.06        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       10.13        75.12        71.74        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
        7.10         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       12.43        11.61        37.15         7.50        12.53        34.82 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 
        4.04         5.03         1.02        24.36         2.01        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       20.35        15.78        17.79        12.89        13.84        22.06 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
        0.92        19.50         7.76         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       14.93        17.92         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        6.38        21.60        10.85         0.23        12.95        49.38 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       21.90        15.35        19.82        23.80        15.65        41.33 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
        3.62        43.79        15.81        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
        2.47        12.00         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
        6.02        11.11         7.40         9.44         8.05        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        7.56         9.14        12.92        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       15.45        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       21.24        23.08        22.85        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-Z5-AAPL 
       13.81        12.99        12.03        13.32        12.76         0.69 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.13               0.23 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             68.52              84.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            15.550             13.825 
[1] "0.1 - 68.5 (15.6)" "0.2 - 84.1 (13.8)"
[1] "hr=" "1.4"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  20P GAIN MUTATED         0        1        5         4        23         0
  20P GAIN WILD-TYPE       1        5        8        22        94         5
                    vv
clus                 STAGE IV
  20P GAIN MUTATED          0
  20P GAIN WILD-TYPE        4
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  5
  STAGE IB                 5                  8
  STAGE IIA                4                 22
  STAGE IIB               23                 94
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED     1   7  25   0
  20P GAIN WILD-TYPE   7  14 114   4
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                1                  7
  T2                7                 14
  T3               25                114
  T4                0                  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"
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     9  23
  20P GAIN WILD-TYPE  36 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      9   23
  20P GAIN WILD-TYPE   36  101
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                9                 36
  1               23                101
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   10  0
  20P GAIN WILD-TYPE 70  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     10    0
  20P GAIN WILD-TYPE   70    4
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               10                 70
  1                0                  4
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   12 22
  20P GAIN WILD-TYPE 66 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12   22
  20P GAIN WILD-TYPE   66   73
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               12                 66
  MALE                 22                 73
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20P GAIN MUTATED                                    24
  20P GAIN WILD-TYPE                                 121
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20P GAIN MUTATED                                       8
  20P GAIN WILD-TYPE                                    14
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  20P GAIN MUTATED                                                  1
  20P GAIN WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  20P GAIN MUTATED                                     1
  20P GAIN WILD-TYPE                                   0
D36V8, multiclass
                                                  clus
vv                                                 20P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 20P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             121
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D36V9, continuous
D36V10, continuous
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   20 10  0  2
  20P GAIN WILD-TYPE 88 41  2  2
D36V11, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               20                 88
  R1               10                 41
  R2                0                  2
  RX                2                  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"
D36V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         1    31
  20P GAIN WILD-TYPE     3                         6   127
D36V13, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   31                127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1  26
  20P GAIN WILD-TYPE   2 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   26
  20P GAIN WILD-TYPE    2  109
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               26                109
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   23 19
  20Q GAIN WILD-TYPE 56 73
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                42                129 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                19                 73 
$`20Q GAIN MUTATED`
TCGA-2J-AAB6 TCGA-2J-AABF TCGA-2J-AABP TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 
        9.63        22.72        11.84         9.60        45.47        20.84 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-FB-A545 
       68.52        63.85        30.64        31.79        12.39        24.07 
TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ6 TCGA-FZ-5921 
       14.76        15.95        23.54        15.55         8.02         5.10 
TCGA-FZ-5926 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-HZ-A77O 
       17.79        21.73         0.92         0.13         3.95         5.26 
TCGA-HZ-A77Q TCGA-IB-7646 TCGA-IB-7886 TCGA-IB-7890 TCGA-IB-8127 TCGA-IB-A5SP 
        1.08         4.77         4.04        19.66        17.16        15.85 
TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A8F3 
       21.90         8.22        15.88         8.05         9.14        12.46 
TCGA-M8-A5N4 TCGA-S4-A8RO TCGA-US-A776 TCGA-US-A77E TCGA-YB-A89D TCGA-YY-A8LH 
       19.20        17.26        27.75        14.14        11.51        66.28 

$`20Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABT 
       22.26        31.86        15.91        14.47        14.40        10.49 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       53.00        23.61         7.36        24.26        28.73        60.95 
TCGA-3A-A9IL TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY 
       84.10        50.70        15.06        34.09        10.13        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A78T TCGA-FB-A7DR 
       19.27         3.12        17.00         5.88        12.43        11.61 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        12.53        34.82         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 
        1.02        24.36         2.01        36.20        20.35        15.78 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       12.89        13.84        22.06        19.50         7.76         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A8P1 
       16.14        10.13         6.38        21.60        10.85         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       12.95        49.38        21.90        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 
       15.65        41.33         3.62        43.79        15.81        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS 
        3.85        15.98         2.47        12.00         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
       20.88         1.35         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         9.44        13.28         7.56 
TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.92        10.29         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40         0.30        21.24        23.08        22.85 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YH-A8SY TCGA-Z5-AAPL 
       13.32        12.76         0.69 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.13               0.23 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             68.52              84.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             15.70              13.81 
[1] "0.1 - 68.5 (15.7)" "0.2 - 84.1 (13.8)"
[1] "hr=" "1.3"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  20Q GAIN MUTATED         0        1        5         7        28         1
  20Q GAIN WILD-TYPE       1        5        8        19        89         4
                    vv
clus                 STAGE IV
  20Q GAIN MUTATED          0
  20Q GAIN WILD-TYPE        4
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  5
  STAGE IB                 5                  8
  STAGE IIA                7                 19
  STAGE IIB               28                 89
  STAGE III                1                  4
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED     1   7  34   0
  20Q GAIN WILD-TYPE   7  14 105   4
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                1                  7
  T2                7                 14
  T3               34                105
  T4                0                  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"
D37V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   12 29
  20Q GAIN WILD-TYPE 33 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     12   29
  20Q GAIN WILD-TYPE   33   95
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               12                 33
  1               29                 95
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   17  0
  20Q GAIN WILD-TYPE 63  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     17    0
  20Q GAIN WILD-TYPE   63    4
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               17                 63
  1                0                  4
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   15 28
  20Q GAIN WILD-TYPE 63 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     15   28
  20Q GAIN WILD-TYPE   63   67
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               15                 63
  MALE                 28                 67
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20Q GAIN MUTATED                                    33
  20Q GAIN WILD-TYPE                                 112
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20Q GAIN MUTATED                                       8
  20Q GAIN WILD-TYPE                                    14
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  20Q GAIN MUTATED                                                  1
  20Q GAIN WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  20Q GAIN MUTATED                                     1
  20Q GAIN WILD-TYPE                                   0
D37V8, multiclass
                                                  clus
vv                                                 20Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            33
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 20Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             112
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D37V9, continuous
D37V10, continuous
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED   26 12  1  2
  20Q GAIN WILD-TYPE 82 39  1  2
D37V11, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               26                 82
  R1               12                 39
  R2                1                  1
  RX                2                  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"
D37V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       0                         1    39
  20Q GAIN WILD-TYPE     3                         6   119
D37V13, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   39                119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     1  33
  20Q GAIN WILD-TYPE   2 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1   33
  20Q GAIN WILD-TYPE    2  102
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               33                102
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    2  6
  22Q GAIN WILD-TYPE 77 86
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                163 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 6                 86 
$`22Q GAIN MUTATED`
TCGA-2J-AABP TCGA-FB-A545 TCGA-FZ-5921 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-IB-7893 
       11.84        24.07         5.10         0.13         3.95         3.85 
TCGA-LB-A7SX TCGA-RB-A7B8 
       12.92        15.32 

$`22Q GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
        3.39        12.95         9.60        45.47        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        30.64        15.06        31.79 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.70        19.46         7.10         7.66        19.27         3.12 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP 
       17.00         5.88        14.76        12.43        11.61        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       37.15         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
        4.04         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       22.06        21.73         0.92        19.50         7.76         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       15.35        19.82        23.80        15.65        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 
        3.62        43.79        15.81        19.66        21.30        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 
        9.44         8.05        13.28         7.56         9.14        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        9.40         0.30        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       27.75        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.13               0.23 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             24.07              84.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              8.47              14.47 
[1] "0.1 - 24.1 (8.5)"  "0.2 - 84.1 (14.5)"
[1] "hr=" "2.6"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  22Q GAIN MUTATED         0        0        0         1         7         0
  22Q GAIN WILD-TYPE       1        6       13        25       110         5
                    vv
clus                 STAGE IV
  22Q GAIN MUTATED          0
  22Q GAIN WILD-TYPE        4
D38V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                1                 25
  STAGE IIB                7                110
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED     0   0   8   0
  22Q GAIN WILD-TYPE   8  21 131   4
D38V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                0                  8
  T2                0                 21
  T3                8                131
  T4                0                  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"
D38V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1   7
  22Q GAIN WILD-TYPE  44 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    7
  22Q GAIN WILD-TYPE   44  117
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                1                 44
  1                7                117
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  0
  22Q GAIN WILD-TYPE 76  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    0
  22Q GAIN WILD-TYPE   76    4
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                4                 76
  1                0                  4
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    6  2
  22Q GAIN WILD-TYPE 72 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      6    2
  22Q GAIN WILD-TYPE   72   93
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                6                 72
  MALE                  2                 93
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  22Q GAIN MUTATED                                     6
  22Q GAIN WILD-TYPE                                 139
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  22Q GAIN MUTATED                                       1
  22Q GAIN WILD-TYPE                                    21
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  22Q GAIN MUTATED                                                  0
  22Q GAIN WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  22Q GAIN MUTATED                                     1
  22Q GAIN WILD-TYPE                                   0
D38V8, multiclass
                                                  clus
vv                                                 22Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 22Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             139
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D38V9, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 53 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABI         TCGA-2J-AABO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2J-AABV         TCGA-2L-AAQA         TCGA-2L-AAQE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-3A-A9I9         TCGA-3A-A9IB         TCGA-3A-A9IJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-6880         TCGA-F2-A8YN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H6-A45N 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7886 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8126 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-IB-AAUU 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-YY-A8LH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D38V10, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 44 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2J-AABI         TCGA-2J-AABO         TCGA-3A-A9IB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-3A-A9IJ         TCGA-3A-A9IR         TCGA-3A-A9IX 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H8-A6C1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7891 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-US-A774         TCGA-XD-AAUI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-YY-A8LH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED     4   2   0   0
  22Q GAIN WILD-TYPE 104  49   2   4
D38V11, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                4                104
  R1                2                 49
  R2                0                  2
  RX                0                  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"
D38V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         1     6
  22Q GAIN WILD-TYPE     3                         6   152
D38V13, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    6                152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0   6
  22Q GAIN WILD-TYPE   3 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    6
  22Q GAIN WILD-TYPE    3  129
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                6                129
[1] 2 2
[1] FALSE

Clustering(39) Variable = XP GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED    7  1
  XP GAIN WILD-TYPE 72 91
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               163 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                91 
$`XP GAIN MUTATED`
TCGA-2J-AAB8 TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IV TCGA-FB-AAPZ 
        2.63        45.47        68.52        63.85        31.79        23.54 
TCGA-LB-A7SX TCGA-US-A776 
       12.92        27.75 

$`XP GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.72        22.26        31.86        15.91        14.47        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IR 
        7.36        24.26        28.73        60.95        84.10        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       30.64        15.06        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
       19.27         3.12        17.00         5.88        24.07        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       12.43        11.61        15.95        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       34.82        15.55         4.04         5.03         1.02         8.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 
       24.36         2.01         5.10        36.20        20.35        15.78 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
       17.79        12.89        13.84        22.06        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
       19.50         7.76         0.13         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
       12.43        14.93        17.92         4.96        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        0.23        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       19.82        23.80        15.65        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 
        9.44         8.05        13.28         7.56         9.14        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       22.85        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             2.63              0.13 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            68.52             84.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            29.77             13.84 
[1] "2.6 - 68.5 (29.8)" "0.1 - 84.1 (13.8)"
[1] "hr=" "9"  
D39V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  XP GAIN MUTATED         0        0        2         1         4         0
  XP GAIN WILD-TYPE       1        6       11        25       113         5
                   vv
clus                STAGE IV
  XP GAIN MUTATED          0
  XP GAIN WILD-TYPE        4
D39V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                2                11
  STAGE IIA               1                25
  STAGE IIB               4               113
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP GAIN MUTATED     0   3   4   0
  XP GAIN WILD-TYPE   8  18 135   4
D39V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               0                 8
  T2               3                18
  T3               4               135
  T4               0                 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"
D39V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     2   4
  XP GAIN WILD-TYPE  43 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    4
  XP GAIN WILD-TYPE   43  120
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               2                43
  1               4               120
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    1  0
  XP GAIN WILD-TYPE 79  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1    0
  XP GAIN WILD-TYPE   79    4
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               1                79
  1               0                 4
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    3  5
  XP GAIN WILD-TYPE 75 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3    5
  XP GAIN WILD-TYPE   75   90
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               3                75
  MALE                 5                90
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XP GAIN MUTATED                                     3
  XP GAIN WILD-TYPE                                 142
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XP GAIN MUTATED                                       4
  XP GAIN WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  XP GAIN MUTATED                                                  1
  XP GAIN WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  XP GAIN MUTATED                                     0
  XP GAIN WILD-TYPE                                   1
D39V8, multiclass
                                                  clus
vv                                                 XP GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 XP GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            142
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D39V9, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                53 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-2J-AABI        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IJ 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-6880        TCGA-F2-A8YN        TCGA-FB-A4P5 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-FB-AAPQ 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-YY-A8LH 
"XP GAIN WILD-TYPE" 
D39V10, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                44 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABI 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IR 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-FB-A7DR        TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPY 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-H6-8124        TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7891        TCGA-IB-8126 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YY-A8LH 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED     4   4   0   0
  XP GAIN WILD-TYPE 104  47   2   4
D39V11, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0               4               104
  R1               4                47
  R2               0                 2
  RX               0                 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"
D39V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         1     7
  XP GAIN WILD-TYPE     3                         6   151
D39V13, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   7               151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0   6
  XP GAIN WILD-TYPE   3 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0    6
  XP GAIN WILD-TYPE    3  129
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               6               129
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    9  2
  XQ GAIN WILD-TYPE 70 90
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               11               160 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                90 
$`XQ GAIN MUTATED`
TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IV TCGA-FB-A78T TCGA-FB-AAPZ 
       45.47        68.52        63.85        31.79        12.43        23.54 
TCGA-HZ-8001 TCGA-IB-A7LX TCGA-LB-A7SX TCGA-Q3-AA2A TCGA-S4-A8RO 
       23.21         8.22        12.92         3.12        17.26 

$`XQ GAIN WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
       22.49         3.39        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        30.64        15.06        34.09        10.13        12.39 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.66        19.27         3.12        17.00         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       14.76        11.61        15.95        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       34.82        15.55         4.04         5.03         1.02         8.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 
       24.36         2.01         5.10        36.20        20.35        15.78 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
       17.79        12.89        13.84        22.06        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
       19.50         7.76         0.13         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       14.93        17.92         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       12.95        49.38         4.77        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       23.80        15.65        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
       13.28         7.56         9.14        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        15.45        13.68        15.32         9.40         0.30 
TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       21.24        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             3.12              0.13 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            68.52             84.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            23.21             13.99 
[1] "3.1 - 68.5 (23.2)" "0.1 - 84.1 (14.0)"
[1] "hr=" "5"  
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  XQ GAIN MUTATED         0        0        3         0         7         1
  XQ GAIN WILD-TYPE       1        6       10        26       110         4
                   vv
clus                STAGE IV
  XQ GAIN MUTATED          0
  XQ GAIN WILD-TYPE        4
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                3                10
  STAGE IIA               0                26
  STAGE IIB               7               110
  STAGE III               1                 4
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED     0   3   7   1
  XQ GAIN WILD-TYPE   8  18 132   3
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               0                 8
  T2               3                18
  T3               7               132
  T4               1                 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"
D40V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2   8
  XQ GAIN WILD-TYPE  43 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    8
  XQ GAIN WILD-TYPE   43  116
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               2                43
  1               8               116
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    1  0
  XQ GAIN WILD-TYPE 79  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    0
  XQ GAIN WILD-TYPE   79    4
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               1                79
  1               0                 4
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    7  5
  XQ GAIN WILD-TYPE 71 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7    5
  XQ GAIN WILD-TYPE   71   90
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               7                71
  MALE                 5                90
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XQ GAIN MUTATED                                     8
  XQ GAIN WILD-TYPE                                 137
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XQ GAIN MUTATED                                       4
  XQ GAIN WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  XQ GAIN MUTATED                                                  0
  XQ GAIN WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  XQ GAIN MUTATED                                     0
  XQ GAIN WILD-TYPE                                   1
D40V8, multiclass
                                                  clus
vv                                                 XQ GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 XQ GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            137
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D40V9, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                52 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-2J-AABI        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-6880        TCGA-F2-A8YN        TCGA-FB-A4P5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A7DR        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-7886 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL        TCGA-YY-A8LH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D40V10, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                43 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABI 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A7DR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUV 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-US-A774 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YY-A8LH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED     7   4   0   1
  XQ GAIN WILD-TYPE 101  47   2   3
D40V11, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               7               101
  R1               4                47
  R2               0                 2
  RX               1                 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"
D40V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         1    11
  XQ GAIN WILD-TYPE     3                         6   147
D40V13, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  11               147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  10
  XQ GAIN WILD-TYPE   2 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   10
  XQ GAIN WILD-TYPE    2  125
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              10               125
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   13 21
  1P LOSS WILD-TYPE 66 71
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               137 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21                71 
$`1P LOSS MUTATED`
TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABO TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       22.26        31.86        14.47         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-3A-A9IL TCGA-3A-A9IS TCGA-3E-AAAZ TCGA-FB-A7DR TCGA-FB-AAPP 
       12.95        84.10        30.64        71.74        11.61        15.95 
TCGA-FB-AAPQ TCGA-FB-AAQ0 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5920 TCGA-FZ-5924 
       37.15        15.55         1.02         8.02         2.01        15.78 
TCGA-HZ-8005 TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-8127 
        3.95         5.26         0.23         4.04        15.81        17.16 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-LB-A8F3 
       15.85        15.12         8.22        15.88         4.73        12.46 
TCGA-OE-A75W TCGA-S4-A8RM TCGA-S4-A8RO TCGA-YY-A8LH 
        8.78        21.24        17.26        66.28 

$`1P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT 
       22.22        22.72        15.91        11.84        14.40        10.49 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
        9.11        21.44         9.60        45.47        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN 
       20.84         7.36        24.26        28.73        60.95        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        15.06        31.79        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       12.39        75.12        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.66        19.27         3.12        17.00         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       14.76        12.43         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        4.04         5.03        24.36         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
       17.79        12.89        13.84        22.06        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
       19.50         7.76         0.13         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       14.93        17.92         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 
        6.38        21.60        10.85         1.08        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        4.77        21.90        15.35        19.82        23.80        15.65 
TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
       41.33         3.62        43.79        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.98         2.47        12.00         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        1.35         0.26         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.92        10.29        19.20        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
       15.32         9.40         0.30        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76         0.69 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.23              0.13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            84.10             75.12 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           15.335            13.840 
[1] "0.2 - 84.1 (15.3)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  1P LOSS MUTATED         1        1        3         8        20         1
  1P LOSS WILD-TYPE       0        5       10        18        97         4
                   vv
clus                STAGE IV
  1P LOSS MUTATED          0
  1P LOSS WILD-TYPE        4
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                1                 5
  STAGE IB                3                10
  STAGE IIA               8                18
  STAGE IIB              20                97
  STAGE III               1                 4
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED     2   4  27   1
  1P LOSS WILD-TYPE   6  17 112   3
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               2                 6
  T2               4                17
  T3              27               112
  T4               1                 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"
D41V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    12  20
  1P LOSS WILD-TYPE  33 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     12   20
  1P LOSS WILD-TYPE   33  104
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              12                33
  1              20               104
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   14  0
  1P LOSS WILD-TYPE 66  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     14    0
  1P LOSS WILD-TYPE   66    4
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              14                66
  1               0                 4
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   11 23
  1P LOSS WILD-TYPE 67 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     11   23
  1P LOSS WILD-TYPE   67   72
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              11                67
  MALE                23                72
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1P LOSS MUTATED                                    29
  1P LOSS WILD-TYPE                                 116
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1P LOSS MUTATED                                       4
  1P LOSS WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  1P LOSS MUTATED                                                  1
  1P LOSS WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  1P LOSS MUTATED                                     0
  1P LOSS WILD-TYPE                                   1
D41V8, multiclass
                                                  clus
vv                                                 1P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           29
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 1P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D41V9, continuous
D41V10, continuous
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   24  9  0  0
  1P LOSS WILD-TYPE 84 42  2  4
D41V11, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              24                84
  R1               9                42
  R2               0                 2
  RX               0                 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"
D41V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         2    31
  1P LOSS WILD-TYPE     2                         5   127
D41V13, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  31               127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1  25
  1P LOSS WILD-TYPE   2 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   25
  1P LOSS WILD-TYPE    2  110
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              25               110
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    4  4
  1Q LOSS WILD-TYPE 75 88
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8               163 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                88 
$`1Q LOSS MUTATED`
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-3A-A9IL TCGA-3A-A9IS TCGA-HZ-8005 TCGA-IB-7889 
        4.70        22.49        84.10        30.64         3.95        15.81 
TCGA-IB-A5SP TCGA-IB-A7M4 
       15.85        15.88 

$`1Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQI 
       11.84        14.40        10.49         9.11        21.44         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       12.95         9.60        45.47        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        24.26        28.73        60.95        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        15.06        31.79        34.09        10.13        12.39 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.66        19.27         3.12        17.00         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       14.76        12.43        11.61        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       20.35        15.78        17.79        12.89        13.84        22.06 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       21.73         0.92        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       15.35        19.82        23.80        15.65        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
        3.62        43.79        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        17.16        12.00         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35         8.22         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
       13.28         7.56         9.14        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        9.40         0.30        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       27.75        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             3.95              0.13 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            84.10             75.12 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           15.865            13.840 
[1] "4.0 - 84.1 (15.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  1Q LOSS MUTATED         1        0        1         1         5         0
  1Q LOSS WILD-TYPE       0        6       12        25       112         5
                   vv
clus                STAGE IV
  1Q LOSS MUTATED          0
  1Q LOSS WILD-TYPE        4
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 6
  STAGE IB                1                12
  STAGE IIA               1                25
  STAGE IIB               5               112
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED     1   1   6   0
  1Q LOSS WILD-TYPE   7  20 133   4
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               1                 7
  T2               1                20
  T3               6               133
  T4               0                 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"
D42V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2   5
  1Q LOSS WILD-TYPE  43 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    5
  1Q LOSS WILD-TYPE   43  119
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               2                43
  1               5               119
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  0
  1Q LOSS WILD-TYPE 77  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE   77    4
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               3                77
  1               0                 4
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    2  6
  1Q LOSS WILD-TYPE 76 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    6
  1Q LOSS WILD-TYPE   76   89
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               2                76
  MALE                 6                89
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1Q LOSS MUTATED                                     6
  1Q LOSS WILD-TYPE                                 139
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1Q LOSS MUTATED                                       2
  1Q LOSS WILD-TYPE                                    20
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  1Q LOSS MUTATED                                                  0
  1Q LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  1Q LOSS MUTATED                                     0
  1Q LOSS WILD-TYPE                                   1
D42V8, multiclass
                                                  clus
vv                                                 1Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 1Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            139
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           20
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D42V9, continuous
D42V10, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                44 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FB-A7DR        TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H6-8124        TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7891        TCGA-IB-8126 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YY-A8LH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     5   3   0   0
  1Q LOSS WILD-TYPE 103  48   2   4
D42V11, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               5               103
  R1               3                48
  R2               0                 2
  RX               0                 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"
D42V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0     8
  1Q LOSS WILD-TYPE     3                         7   150
D42V13, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   8               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   5
  1Q LOSS WILD-TYPE   3 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    5
  1Q LOSS WILD-TYPE    3  130
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               130
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    6  5
  2P LOSS WILD-TYPE 73 87
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               160 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5                87 
$`2P LOSS MUTATED`
TCGA-2J-AABP TCGA-3A-A9I9 TCGA-3A-A9IL TCGA-3A-A9IS TCGA-H6-8124 TCGA-HZ-7289 
       11.84        20.84        84.10        30.64        12.89        21.73 
TCGA-HZ-A49I TCGA-IB-7646 TCGA-IB-7652 TCGA-IB-7888 TCGA-US-A776 
       10.13         4.77        23.80        43.79        27.75 

$`2P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
        3.39        12.95         9.60        45.47        53.00        23.61 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        24.26        28.73        60.95        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        15.06        31.79        34.09        10.13        12.39 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.66        19.27         3.12        17.00         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       14.76        12.43        11.61        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
       20.35        15.78        17.79        13.84        22.06         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
       19.50         7.76         0.13         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
       12.43        14.93        17.92         4.96        21.70        16.14 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 
       12.95        49.38        21.90        15.35        19.82        15.65 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       41.33         4.04         3.62        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       11.11         7.40         9.44         8.05        13.28         7.56 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        9.14        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       15.45        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E 
       21.24        17.26        23.08        22.85        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             4.77              0.13 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            84.10             75.12 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            21.73             13.99 
[1] "4.8 - 84.1 (21.7)" "0.1 - 75.1 (14.0)"
[1] "hr=" "1.9"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  2P LOSS MUTATED         1        0        1         3         6         0
  2P LOSS WILD-TYPE       0        6       12        23       111         5
                   vv
clus                STAGE IV
  2P LOSS MUTATED          0
  2P LOSS WILD-TYPE        4
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 6
  STAGE IB                1                12
  STAGE IIA               3                23
  STAGE IIB               6               111
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     1   1   9   0
  2P LOSS WILD-TYPE   7  20 130   4
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               1                 7
  T2               1                20
  T3               9               130
  T4               0                 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"
D43V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     4   6
  2P LOSS WILD-TYPE  41 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    6
  2P LOSS WILD-TYPE   41  118
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               4                41
  1               6               118
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    5  0
  2P LOSS WILD-TYPE 75  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    0
  2P LOSS WILD-TYPE   75    4
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               5                75
  1               0                 4
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    5  6
  2P LOSS WILD-TYPE 73 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    6
  2P LOSS WILD-TYPE   73   89
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               5                73
  MALE                 6                89
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2P LOSS MUTATED                                     6
  2P LOSS WILD-TYPE                                 139
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2P LOSS MUTATED                                       3
  2P LOSS WILD-TYPE                                    19
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  2P LOSS MUTATED                                                  1
  2P LOSS WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  2P LOSS MUTATED                                     1
  2P LOSS WILD-TYPE                                   0
D43V8, multiclass
                                                  clus
vv                                                 2P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 2P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            139
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D43V9, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                52 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2J-AABI        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F2-6880        TCGA-F2-A8YN        TCGA-FB-A4P5        TCGA-FB-A5VM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FB-AAPY        TCGA-H6-A45N        TCGA-H8-A6C1        TCGA-HZ-A77Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644        TCGA-IB-7649 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7887 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-IB-AAUV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL        TCGA-YY-A8LH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V10, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                44 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FB-A7DR        TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YY-A8LH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     7   3   0   1
  2P LOSS WILD-TYPE 101  48   2   3
D43V11, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               7               101
  R1               3                48
  R2               0                 2
  RX               1                 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"
D43V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       1                         1     9
  2P LOSS WILD-TYPE     2                         6   149
D43V13, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   9               149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  10
  2P LOSS WILD-TYPE   3 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   10
  2P LOSS WILD-TYPE    3  125
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              10               125
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    4  1
  2Q LOSS WILD-TYPE 75 91
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               166 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                91 
$`2Q LOSS MUTATED`
TCGA-3A-A9IL TCGA-3A-A9IS TCGA-H6-8124 TCGA-IB-7646 TCGA-US-A776 
       84.10        30.64        12.89         4.77        27.75 

$`2Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 
       22.49         3.39        12.95         9.60        45.47        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       23.61        20.84         7.36        24.26        28.73        60.95 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        63.85        50.70        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP 
        5.88        24.07        14.76        12.43        11.61        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       37.15         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
        4.04         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-A45N 
        5.10        36.20        20.35        15.78        17.79        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       22.06        21.73         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       21.90        15.35        19.82        23.80        15.65        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       11.11         7.40         9.44         8.05        13.28         7.56 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        9.14        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       15.45        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E 
       21.24        17.26        23.08        22.85        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             4.77              0.13 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            84.10             75.12 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           27.750            14.155 
[1] "4.8 - 84.1 (27.8)" "0.1 - 75.1 (14.2)"
[1] "hr=" "4.8"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  2Q LOSS MUTATED         1        0        1         1         2         0
  2Q LOSS WILD-TYPE       0        6       12        25       115         5
                   vv
clus                STAGE IV
  2Q LOSS MUTATED          0
  2Q LOSS WILD-TYPE        4
D44V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 6
  STAGE IB                1                12
  STAGE IIA               1                25
  STAGE IIB               2               115
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     1   1   3   0
  2Q LOSS WILD-TYPE   7  20 136   4
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               1                 7
  T2               1                20
  T3               3               136
  T4               0                 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"
D44V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2   2
  2Q LOSS WILD-TYPE  43 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    2
  2Q LOSS WILD-TYPE   43  122
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               2                43
  1               2               122
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    2  0
  2Q LOSS WILD-TYPE 78  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    0
  2Q LOSS WILD-TYPE   78    4
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               2                78
  1               0                 4
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    2  3
  2Q LOSS WILD-TYPE 76 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    3
  2Q LOSS WILD-TYPE   76   92
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               2                76
  MALE                 3                92
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2Q LOSS MUTATED                                     2
  2Q LOSS WILD-TYPE                                 143
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2Q LOSS MUTATED                                       2
  2Q LOSS WILD-TYPE                                    20
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  2Q LOSS MUTATED                                                  1
  2Q LOSS WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  2Q LOSS MUTATED                                     0
  2Q LOSS WILD-TYPE                                   1
D44V8, multiclass
                                                  clus
vv                                                 2Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 2Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            143
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           20
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D44V9, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                53 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2J-AABI        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-6880        TCGA-F2-A8YN        TCGA-FB-A4P5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-FB-AAPQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-A45N        TCGA-H8-A6C1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-7886 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-YY-A8LH 
"2Q LOSS WILD-TYPE" 
D44V10, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                44 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FB-A7DR        TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YY-A8LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     4   1   0   0
  2Q LOSS WILD-TYPE 104  50   2   4
D44V11, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               4               104
  R1               1                50
  R2               0                 2
  RX               0                 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"
D44V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0     5
  2Q LOSS WILD-TYPE     3                         7   153
D44V13, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   5               153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   5
  2Q LOSS WILD-TYPE   3 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    5
  2Q LOSS WILD-TYPE    3  130
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               130
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   16 19
  3P LOSS WILD-TYPE 63 73
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               35               136 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               19                73 
$`3P LOSS MUTATED`
TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQI TCGA-2L-AAQJ 
       31.86        14.47        11.84         9.11         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IC TCGA-3A-A9IO TCGA-F2-A44H 
        9.60        45.47        53.00        24.26        63.85        19.27 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPY TCGA-FB-AAQ1 TCGA-FB-AAQ6 TCGA-FZ-5924 
       15.95        37.15        34.82         4.04         8.02        15.78 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8005 TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A8P1 
        0.92        20.19         3.95        21.60         5.26         0.23 
TCGA-IB-7647 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7LX 
       21.90         4.04         3.62        17.16        15.85         8.22 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-RB-AA9M TCGA-YY-A8LH 
        8.05        12.92        12.46         9.40        66.28 

$`3P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABT 
       22.22        22.72        22.26        15.91        14.40        10.49 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       21.44         4.70        22.49        23.61        20.84         7.36 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS 
       28.73        60.95        84.10        68.52        50.70        30.64 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        31.79        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
        3.12        17.00         5.88        24.07        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 
       11.61         7.50        12.53        23.54        15.55         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 
       17.79        12.89        13.84        22.06        21.73        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 
        7.76         0.13         0.26        27.62        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A77P 
        4.96        21.70        16.14        10.13         6.38        10.85 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 
        1.08        12.95        49.38         4.77        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        15.65        41.33        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ 
       21.30         3.85        15.98         2.47        12.00         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.12        20.88        21.90         1.35        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        9.44        13.28         7.56         9.14        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS 
        8.78        15.45        13.68         3.12        15.32         0.30 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       14.14         0.39        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       13.32        11.51        12.76         0.69 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.23              0.13 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            66.28             84.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           12.950            14.285 
[1] "0.2 - 66.3 (12.9)" "0.1 - 84.1 (14.3)"
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  3P LOSS MUTATED         0        2        1         4        26         1
  3P LOSS WILD-TYPE       1        4       12        22        91         4
                   vv
clus                STAGE IV
  3P LOSS MUTATED          0
  3P LOSS WILD-TYPE        4
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                2                 4
  STAGE IB                1                12
  STAGE IIA               4                22
  STAGE IIB              26                91
  STAGE III               1                 4
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED     3   3  27   1
  3P LOSS WILD-TYPE   5  18 112   3
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               3                 5
  T2               3                18
  T3              27               112
  T4               1                 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"
D45V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    8 26
  3P LOSS WILD-TYPE 37 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      8   26
  3P LOSS WILD-TYPE   37   98
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               8                37
  1              26                98
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   13  0
  3P LOSS WILD-TYPE 67  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     13    0
  3P LOSS WILD-TYPE   67    4
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              13                67
  1               0                 4
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    9 26
  3P LOSS WILD-TYPE 69 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      9   26
  3P LOSS WILD-TYPE   69   69
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               9                69
  MALE                26                69
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3P LOSS MUTATED                                    30
  3P LOSS WILD-TYPE                                 115
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3P LOSS MUTATED                                       4
  3P LOSS WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  3P LOSS MUTATED                                                  0
  3P LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  3P LOSS MUTATED                                     1
  3P LOSS WILD-TYPE                                   0
D45V8, multiclass
                                                  clus
vv                                                 3P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           30
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 3P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D45V9, continuous
D45V10, continuous
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED   22 12  0  1
  3P LOSS WILD-TYPE 86 39  2  3
D45V11, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              22                86
  R1              12                39
  R2               0                 2
  RX               1                 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"
D45V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         2    33
  3P LOSS WILD-TYPE     3                         5   125
D45V13, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  33               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0  26
  3P LOSS WILD-TYPE   3 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   26
  3P LOSS WILD-TYPE    3  109
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              26               109
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   11  8
  3Q LOSS WILD-TYPE 68 84
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19               152 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8                84 
$`3Q LOSS MUTATED`
TCGA-2J-AABP TCGA-2L-AAQI TCGA-2L-AAQM TCGA-3A-A9IO TCGA-3A-A9IS TCGA-F2-A44H 
       11.84         3.39        45.47        63.85        30.64        19.27 
TCGA-FB-AAPP TCGA-FB-AAPY TCGA-FZ-5920 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A8P1 
       15.95        34.82         2.01        20.19         5.26         0.23 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
        4.04        17.16        15.85         8.05        12.92        12.46 
TCGA-YY-A8LH 
       66.28 

$`3Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        53.00        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IR 
       24.26        28.73        60.95        84.10        68.52        50.70 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        31.79        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
        3.12        17.00         5.88        24.07        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       11.61        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5921 
        4.04         5.03         1.02         8.02        24.36         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       22.06        21.73         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.26        27.62        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        3.95         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P 
       21.70        16.14        10.13         6.38        21.60        10.85 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        1.08        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 
       19.82        23.80        15.65        41.33         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         9.44        13.28         7.56 
TCGA-L1-A7W4 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
        9.14        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO 
        3.12        15.32         9.40         0.30        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76         0.69 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.23              0.13 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            66.28             84.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           15.850            14.155 
[1] "0.2 - 66.3 (15.8)" "0.1 - 84.1 (14.2)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  3Q LOSS MUTATED         0        0        2         3        13         0
  3Q LOSS WILD-TYPE       1        6       11        23       104         5
                   vv
clus                STAGE IV
  3Q LOSS MUTATED          0
  3Q LOSS WILD-TYPE        4
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                2                11
  STAGE IIA               3                23
  STAGE IIB              13               104
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED     0   4  14   0
  3Q LOSS WILD-TYPE   8  17 125   4
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                 8
  T2               4                17
  T3              14               125
  T4               0                 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"
D46V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  13
  3Q LOSS WILD-TYPE  40 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   13
  3Q LOSS WILD-TYPE   40  111
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               5                40
  1              13               111
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    7  0
  3Q LOSS WILD-TYPE 73  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      7    0
  3Q LOSS WILD-TYPE   73    4
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               7                73
  1               0                 4
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    5 14
  3Q LOSS WILD-TYPE 73 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   14
  3Q LOSS WILD-TYPE   73   81
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               5                73
  MALE                14                81
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3Q LOSS MUTATED                                    15
  3Q LOSS WILD-TYPE                                 130
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3Q LOSS MUTATED                                       3
  3Q LOSS WILD-TYPE                                    19
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  3Q LOSS MUTATED                                                  0
  3Q LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  3Q LOSS MUTATED                                     1
  3Q LOSS WILD-TYPE                                   0
D46V8, multiclass
                                                  clus
vv                                                 3Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 3Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            130
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D46V9, continuous
D46V10, continuous
                   vv
clus                R0 R1 R2 RX
  3Q LOSS MUTATED   13  6  0  0
  3Q LOSS WILD-TYPE 95 45  2  4
D46V11, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              13                95
  R1               6                45
  R2               0                 2
  RX               0                 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"
D46V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         3    16
  3Q LOSS WILD-TYPE     3                         4   142
D46V13, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  16               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  15
  3Q LOSS WILD-TYPE   3 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   15
  3Q LOSS WILD-TYPE    3  120
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               120
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    9 14
  4P LOSS WILD-TYPE 70 78
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               148 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               14                78 
$`4P LOSS MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABO TCGA-2L-AAQE TCGA-3A-A9I5 TCGA-3A-A9IB TCGA-3A-A9IC 
        2.63        14.47        22.49        53.00         7.36        24.26 
TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPZ TCGA-FB-AAQ1 
       12.39        71.74        14.76        11.61        23.54         4.04 
TCGA-FB-AAQ2 TCGA-FZ-5920 TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-IB-7886 
        5.03         2.01         0.92        20.19        10.13         4.04 
TCGA-IB-7887 TCGA-IB-A5SP TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUQ 
        3.62        15.85        15.88         7.86         6.02 

$`4P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR 
       22.72        22.26        31.86        15.91        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ 
       10.49         9.11        21.44         4.70         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IH TCGA-3A-A9IJ 
        9.60        45.47        23.61        20.84        28.73        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       84.10        68.52        63.85        50.70        30.64        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 
       31.79        34.09        10.13        75.12        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        5.88        24.07        12.43        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       12.53        34.82        15.55         1.02         8.02        24.36 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 
        5.10        36.20        20.35        15.78        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       13.84        22.06        21.73        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.26        27.62        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        3.95         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       21.70        16.14         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7888 
       15.35        19.82        23.80        15.65        41.33        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       17.16        12.00         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUR 
        1.35         8.22         0.26         4.73        14.17        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       13.68         3.12        15.32         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.92              0.13 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            71.74             84.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           11.610            14.665 
[1] "0.9 - 71.7 (11.6)" "0.1 - 84.1 (14.7)"
[1] "hr=" "1.4"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  4P LOSS MUTATED         0        1        1         3        18         0
  4P LOSS WILD-TYPE       1        5       12        23        99         5
                   vv
clus                STAGE IV
  4P LOSS MUTATED          0
  4P LOSS WILD-TYPE        4
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 5
  STAGE IB                1                12
  STAGE IIA               3                23
  STAGE IIB              18                99
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P LOSS MUTATED     1   2  20   0
  4P LOSS WILD-TYPE   7  19 119   4
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               1                 7
  T2               2                19
  T3              20               119
  T4               0                 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"
D47V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     4  18
  4P LOSS WILD-TYPE  41 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4   18
  4P LOSS WILD-TYPE   41  106
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               4                41
  1              18               106
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   12  0
  4P LOSS WILD-TYPE 68  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     12    0
  4P LOSS WILD-TYPE   68    4
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              12                68
  1               0                 4
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    5 18
  4P LOSS WILD-TYPE 73 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5   18
  4P LOSS WILD-TYPE   73   77
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               5                73
  MALE                18                77
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4P LOSS MUTATED                                    22
  4P LOSS WILD-TYPE                                 123
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4P LOSS MUTATED                                       0
  4P LOSS WILD-TYPE                                    22
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  4P LOSS MUTATED                                                  1
  4P LOSS WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  4P LOSS MUTATED                                     0
  4P LOSS WILD-TYPE                                   1
D47V8, multiclass
                                                  clus
vv                                                 4P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 4P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           22
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D47V9, continuous
D47V10, continuous
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED   13  9  0  0
  4P LOSS WILD-TYPE 95 42  2  4
D47V11, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              13                95
  R1               9                42
  R2               0                 2
  RX               0                 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"
D47V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       1                         1    21
  4P LOSS WILD-TYPE     2                         6   137
D47V13, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  21               137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  18
  4P LOSS WILD-TYPE   2 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   18
  4P LOSS WILD-TYPE    2  117
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              18               117
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    9 13
  4Q LOSS WILD-TYPE 70 79
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               22               149 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               13                79 
$`4Q LOSS MUTATED`
TCGA-2J-AABO TCGA-2L-AAQE TCGA-3A-A9I5 TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-FB-A5VM 
       14.47        22.49        53.00        12.39        71.74        14.76 
TCGA-FB-A7DR TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5920 TCGA-HZ-7925 
       11.61        23.54         4.04         5.03         2.01        20.19 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-IB-7886 TCGA-IB-A5SP TCGA-IB-A7LX TCGA-IB-A7M4 
       10.13         6.38         4.04        15.85         8.22        15.88 
TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-RB-AA9M TCGA-XD-AAUI 
        7.86         6.02         9.40        12.03 

$`4Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABP 
       22.22        22.72        22.26        31.86        15.91        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.40        10.49         9.11        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        28.73        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        30.64        15.06        31.79        34.09        10.13 
TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       75.12        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A78T 
       19.27         3.12        17.00         5.88        24.07        12.43 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        34.82        15.55 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02         8.02        24.36         5.10        36.20        20.35 
TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
       15.78        17.79        12.89        13.84        22.06        21.73 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
        0.92        19.50         7.76         0.13         0.26        27.62 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
       12.43        14.93        17.92         4.96        21.70        16.14 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       15.65        41.33         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM 
        7.20        15.12        20.88        21.90         1.35         0.26 
TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
        4.73        14.17        11.11         7.40         9.44         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
       13.28         7.56         9.14        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2.01              0.13 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            71.74             84.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            11.82             14.93 
[1] "2.0 - 71.7 (11.8)" "0.1 - 84.1 (14.9)"
[1] "hr=" "1.3"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  4Q LOSS MUTATED         0        1        1         3        18         0
  4Q LOSS WILD-TYPE       1        5       12        23        99         5
                   vv
clus                STAGE IV
  4Q LOSS MUTATED          0
  4Q LOSS WILD-TYPE        4
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 5
  STAGE IB                1                12
  STAGE IIA               3                23
  STAGE IIB              18                99
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q LOSS MUTATED     2   2  19   0
  4Q LOSS WILD-TYPE   6  19 120   4
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               2                 6
  T2               2                19
  T3              19               120
  T4               0                 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"
D48V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4  18
  4Q LOSS WILD-TYPE  41 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4   18
  4Q LOSS WILD-TYPE   41  106
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               4                41
  1              18               106
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9  0
  4Q LOSS WILD-TYPE 71  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9    0
  4Q LOSS WILD-TYPE   71    4
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               9                71
  1               0                 4
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    4 19
  4Q LOSS WILD-TYPE 74 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4   19
  4Q LOSS WILD-TYPE   74   76
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               4                74
  MALE                19                76
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4Q LOSS MUTATED                                    22
  4Q LOSS WILD-TYPE                                 123
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4Q LOSS MUTATED                                       0
  4Q LOSS WILD-TYPE                                    22
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  4Q LOSS MUTATED                                                  1
  4Q LOSS WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  4Q LOSS MUTATED                                     0
  4Q LOSS WILD-TYPE                                   1
D48V8, multiclass
                                                  clus
vv                                                 4Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 4Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           22
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D48V9, continuous
D48V10, continuous
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   13  9  0  0
  4Q LOSS WILD-TYPE 95 42  2  4
D48V11, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              13                95
  R1               9                42
  R2               0                 2
  RX               0                 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"
D48V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       1                         1    21
  4Q LOSS WILD-TYPE     2                         6   137
D48V13, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  21               137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2  17
  4Q LOSS WILD-TYPE   1 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   17
  4Q LOSS WILD-TYPE    1  118
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              17               118
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    3  4
  5P LOSS WILD-TYPE 76 88
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               164 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                88 
$`5P LOSS MUTATED`
TCGA-2J-AABO TCGA-2L-AAQI TCGA-FB-A545 TCGA-IB-8127 TCGA-IB-A7M4 TCGA-US-A779 
       14.47         3.39        24.07        17.16        15.88        16.80 
TCGA-XD-AAUI 
       12.03 

$`5P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABP 
       22.22        22.72        22.26        31.86        15.91        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.40        10.49         9.11        21.44         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       12.95         9.60        45.47        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        28.73        60.95        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ 
        5.88        14.76        12.43        11.61        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
        7.50        12.53        34.82        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        5.03         1.02         8.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       22.06        21.73         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        4.77        21.90        15.35        19.82        23.80        15.65 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       21.30         3.85        15.98         2.47        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       13.68         3.12        15.32         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G 
       17.26        23.08        22.85        27.75        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       18.67        13.81        12.99        13.32        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.39              0.13 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            24.07             84.10 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            15.88             13.99 
[1] "3.4 - 24.1 (15.9)" "0.1 - 84.1 (14.0)"
[1] "hr=" "1.2"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  5P LOSS MUTATED         0        0        0         0         7         0
  5P LOSS WILD-TYPE       1        6       13        26       110         5
                   vv
clus                STAGE IV
  5P LOSS MUTATED          0
  5P LOSS WILD-TYPE        4
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                0                13
  STAGE IIA               0                26
  STAGE IIB               7               110
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED     0   0   7   0
  5P LOSS WILD-TYPE   8  21 132   4
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0                 8
  T2               0                21
  T3               7               132
  T4               0                 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"
D49V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0   7
  5P LOSS WILD-TYPE  45 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    7
  5P LOSS WILD-TYPE   45  117
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               0                45
  1               7               117
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    3  0
  5P LOSS WILD-TYPE 77  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3    0
  5P LOSS WILD-TYPE   77    4
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               3                77
  1               0                 4
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    3  4
  5P LOSS WILD-TYPE 75 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3    4
  5P LOSS WILD-TYPE   75   91
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               3                75
  MALE                 4                91
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5P LOSS MUTATED                                     7
  5P LOSS WILD-TYPE                                 138
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5P LOSS MUTATED                                       0
  5P LOSS WILD-TYPE                                    22
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  5P LOSS MUTATED                                                  0
  5P LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  5P LOSS MUTATED                                     0
  5P LOSS WILD-TYPE                                   1
D49V8, multiclass
                                                  clus
vv                                                 5P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 5P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            138
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           22
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D49V9, continuous
D49V10, continuous
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED     3   3   0   0
  5P LOSS WILD-TYPE 105  48   2   4
D49V11, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               3               105
  R1               3                48
  R2               0                 2
  RX               0                 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"
D49V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     7
  5P LOSS WILD-TYPE     3                         7   151
D49V13, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   7               151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0   5
  5P LOSS WILD-TYPE   3 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    5
  5P LOSS WILD-TYPE    3  130
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               130
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    4  6
  5Q LOSS WILD-TYPE 75 86
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10               161 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                86 
$`5Q LOSS MUTATED`
TCGA-2J-AABO TCGA-2J-AABP TCGA-FB-A545 TCGA-HZ-7289 TCGA-HZ-8005 TCGA-IB-8127 
       14.47        11.84        24.07        21.73         3.95        17.16 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-US-A779 TCGA-XD-AAUI 
        1.35        15.88        16.80        12.03 

$`5Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABR 
       22.22        22.72        22.26        31.86        15.91        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       12.95         9.60        45.47        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        28.73        60.95        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ 
        5.88        14.76        12.43        11.61        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
        7.50        12.53        34.82        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        5.03         1.02         8.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       22.06         0.92        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       15.35        19.82        23.80        15.65        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98         2.47        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88        21.90         8.22         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
       13.28         7.56         9.14        12.92        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        9.40         0.30        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       27.75        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1.35              0.13 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            24.07             84.10 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           15.175            14.140 
[1] "1.4 - 24.1 (15.2)" "0.1 - 84.1 (14.1)"
[1] "hr=" "1.3"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  5Q LOSS MUTATED         0        0        0         0        10         0
  5Q LOSS WILD-TYPE       1        6       13        26       107         5
                   vv
clus                STAGE IV
  5Q LOSS MUTATED          0
  5Q LOSS WILD-TYPE        4
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 6
  STAGE IB                0                13
  STAGE IIA               0                26
  STAGE IIB              10               107
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED     0   0  10   0
  5Q LOSS WILD-TYPE   8  21 129   4
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0                 8
  T2               0                21
  T3              10               129
  T4               0                 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"
D50V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  10
  5Q LOSS WILD-TYPE  45 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   10
  5Q LOSS WILD-TYPE   45  114
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               0                45
  1              10               114
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    5  0
  5Q LOSS WILD-TYPE 75  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    0
  5Q LOSS WILD-TYPE   75    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               5                75
  1               0                 4
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    4  6
  5Q LOSS WILD-TYPE 74 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4    6
  5Q LOSS WILD-TYPE   74   89
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               4                74
  MALE                 6                89
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5Q LOSS MUTATED                                     8
  5Q LOSS WILD-TYPE                                 137
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5Q LOSS MUTATED                                       1
  5Q LOSS WILD-TYPE                                    21
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  5Q LOSS MUTATED                                                  0
  5Q LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  5Q LOSS MUTATED                                     1
  5Q LOSS WILD-TYPE                                   0
D50V8, multiclass
                                                  clus
vv                                                 5Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 5Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            137
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D50V9, continuous
D50V10, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED     4   4   0   1
  5Q LOSS WILD-TYPE 104  47   2   3
D50V11, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               4               104
  R1               4                47
  R2               0                 2
  RX               1                 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"
D50V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         0    10
  5Q LOSS WILD-TYPE     3                         7   148
D50V13, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  10               148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0   8
  5Q LOSS WILD-TYPE   3 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    8
  5Q LOSS WILD-TYPE    3  127
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               8               127
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   20 39
  6P LOSS WILD-TYPE 59 53
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               59               112 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               39                53 
$`6P LOSS MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
        2.17        23.97        31.86        14.47        11.84         9.11 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQM TCGA-3A-A9IB TCGA-3A-A9IC 
        4.70        22.49         3.39        45.47         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IL TCGA-3A-A9IS TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44H 
       28.73        84.10        30.64        71.74        10.98        19.27 
TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       24.07        15.95        34.82        15.55         4.04         5.03 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5924 TCGA-H6-8124 TCGA-HZ-7289 
       24.36         2.01         5.10        15.78        12.89        21.73 
TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-A4BK TCGA-HZ-A77O 
       19.50        20.19        23.21         9.83        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7886 TCGA-IB-7889 
       10.85         1.08         4.77        21.90         4.04        15.81 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UF 
       19.66         3.85        17.16        15.85        15.12        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUO TCGA-LB-A7SX TCGA-OE-A75W TCGA-PZ-A5RE 
        1.35         8.22         7.86        12.92         8.78        15.45 
TCGA-US-A779 TCGA-US-A77G TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.80         0.39        11.51        12.76        66.28 

$`6P LOSS WILD-TYPE`
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF 
        9.63         2.63        20.61        19.96        22.22        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABV TCGA-2L-AAQJ 
       22.26        15.91        14.40        10.49        21.44        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IJ TCGA-3A-A9IN 
        9.60        53.00        23.61        20.84        60.95        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        15.06        31.79        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       12.39        75.12         9.70        19.46         7.10         7.66 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR 
        3.12        17.00         5.88        14.76        12.43        11.61 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       37.15         7.50        12.53        23.54         1.02         8.02 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
       36.20        20.35        17.79        13.84        22.06         0.92 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8002 
        7.76         0.13         0.26        27.62        17.03        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        0.69         3.95        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A8P1 TCGA-IB-7644 
       21.70        16.14        10.13         6.38         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       49.38        15.35        19.82        23.80        15.65        41.33 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
        3.62        43.79        21.30        15.98         2.47        12.00 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP 
        7.20        20.88        15.88         0.26         4.73        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
        6.02        11.11         7.40         9.44         8.05        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-Q3-A5QY 
        7.56         9.14        12.46        10.29        19.20        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO 
        3.12        15.32         9.40         0.30        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUG 
       23.08        22.85        27.75        14.14        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-Z5-AAPL 
       12.99        12.03        13.32         0.69 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.39              0.13 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            84.10             75.12 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           15.450            13.825 
[1] "0.4 - 84.1 (15.4)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.3"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  6P LOSS MUTATED         1        1        2         8        45         2
  6P LOSS WILD-TYPE       0        5       11        18        72         3
                   vv
clus                STAGE IV
  6P LOSS MUTATED          0
  6P LOSS WILD-TYPE        4
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                1                 5
  STAGE IB                2                11
  STAGE IIA               8                18
  STAGE IIB              45                72
  STAGE III               2                 3
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    2  5 51  1
  6P LOSS WILD-TYPE  6 16 88  3
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                 6
  T2               5                16
  T3              51                88
  T4               1                 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"
D51V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   12 46
  6P LOSS WILD-TYPE 33 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     12   46
  6P LOSS WILD-TYPE   33   78
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              12                33
  1              46                78
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   28  0
  6P LOSS WILD-TYPE 52  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     28    0
  6P LOSS WILD-TYPE   52    4
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              28                52
  1               0                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   23 36
  6P LOSS WILD-TYPE 55 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     23   36
  6P LOSS WILD-TYPE   55   59
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              23                55
  MALE                36                59
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6P LOSS MUTATED                                    46
  6P LOSS WILD-TYPE                                  99
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6P LOSS MUTATED                                      11
  6P LOSS WILD-TYPE                                    11
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  6P LOSS MUTATED                                                  0
  6P LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  6P LOSS MUTATED                                     1
  6P LOSS WILD-TYPE                                   0
D51V8, multiclass
                                                  clus
vv                                                 6P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           46
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 6P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D51V9, continuous
D51V10, continuous
                   vv
clus                R0 R1 R2 RX
  6P LOSS MUTATED   35 17  0  1
  6P LOSS WILD-TYPE 73 34  2  3
D51V11, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              35                73
  R1              17                34
  R2               0                 2
  RX               1                 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"
D51V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       0                         2    55
  6P LOSS WILD-TYPE     3                         5   103
D51V13, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  55               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"
D51V14, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    1 44
  6P LOSS WILD-TYPE  2 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   44
  6P LOSS WILD-TYPE    2   91
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              44                91
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   27 51
  6Q LOSS WILD-TYPE 52 41
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               78                93 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               51                41 
$`6Q LOSS MUTATED`
TCGA-2J-AAB1 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABO 
        2.17        19.96        22.22        22.26        31.86        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQM 
       11.84         9.11         4.70        22.49         3.39        45.47 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IL TCGA-3A-A9IS 
       20.84         7.36        24.26        28.73        84.10        30.64 
TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44H TCGA-FB-A545 
       15.06        10.13        71.74        10.98        19.27        24.07 
TCGA-FB-AAPP TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       15.95        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5924 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
       15.78        12.89        21.73        19.50         0.13        20.19 
TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       23.21         9.83        17.92         5.26        10.85         1.08 
TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       12.95         4.77        21.90        41.33         4.04         3.62 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS 
       15.81        19.66         3.85        17.16        15.85        15.12 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUU 
       21.90         1.35         8.22         4.73         7.86         8.05 
TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-S4-A8RM TCGA-S4-A8RP 
       12.92        19.20         8.78        15.45        21.24        23.08 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       27.75        16.80         0.39        11.51        12.76        66.28 

$`6Q LOSS WILD-TYPE`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABK 
       23.97         9.63         2.63        20.61        22.72        15.91 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABV TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
       14.40        10.49        21.44        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IV 
       23.61        60.95        68.52        63.85        50.70        31.79 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       34.09        12.39        75.12         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T 
        7.66         3.12        17.00         5.88        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FZ-5923 TCGA-FZ-5926 
       11.61        37.15         7.50        12.53        20.35        17.79 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 
       13.84        22.06         0.92         7.76         0.26        27.62 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 
       17.03        12.03         0.69         3.95        12.43        14.93 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        0.23        49.38        15.35        19.82        23.80        15.65 
TCGA-IB-7888 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ 
       43.79        21.30        15.98         2.47        12.00         7.20 
TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       20.88        15.88         0.26        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 
        7.40         9.44        13.28         7.56         9.14        12.46 
TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       17.26        22.85        14.14        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-Z5-AAPL 
       12.03        13.32         0.69 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.13              0.23 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            84.10             75.12 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            15.50             13.68 
[1] "0.1 - 84.1 (15.5)" "0.2 - 75.1 (13.7)"
[1] "hr=" "1.4"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  6Q LOSS MUTATED         1        2        3        14        54         2
  6Q LOSS WILD-TYPE       0        4       10        12        63         3
                   vv
clus                STAGE IV
  6Q LOSS MUTATED          2
  6Q LOSS WILD-TYPE        2
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                2                 4
  STAGE IB                3                10
  STAGE IIA              14                12
  STAGE IIB              54                63
  STAGE III               2                 3
  STAGE IV                2                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    3  6 68  1
  6Q LOSS WILD-TYPE  5 15 71  3
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               3                 5
  T2               6                15
  T3              68                71
  T4               1                 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"
D52V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   21 56
  6Q LOSS WILD-TYPE 24 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21   56
  6Q LOSS WILD-TYPE   24   68
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              21                24
  1              56                68
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   36  2
  6Q LOSS WILD-TYPE 44  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     36    2
  6Q LOSS WILD-TYPE   44    2
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              36                44
  1               2                 2
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   32 46
  6Q LOSS WILD-TYPE 46 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     32   46
  6Q LOSS WILD-TYPE   46   49
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              32                46
  MALE                46                49
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6Q LOSS MUTATED                                    65
  6Q LOSS WILD-TYPE                                  80
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6Q LOSS MUTATED                                      10
  6Q LOSS WILD-TYPE                                    12
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  6Q LOSS MUTATED                                                  1
  6Q LOSS WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  6Q LOSS MUTATED                                     1
  6Q LOSS WILD-TYPE                                   0
D52V8, multiclass
                                                  clus
vv                                                 6Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 6Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             80
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           12
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D52V9, continuous
D52V10, continuous
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED   48 23  0  1
  6Q LOSS WILD-TYPE 60 28  2  3
D52V11, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              48                60
  R1              23                28
  R2               0                 2
  RX               1                 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"
D52V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       0                         2    73
  6Q LOSS WILD-TYPE     3                         5    85
D52V13, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  73                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"
D52V14, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    2 58
  6Q LOSS WILD-TYPE  1 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   58
  6Q LOSS WILD-TYPE    1   77
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              58                77
[1] 2 2
[1] FALSE

Clustering(53) Variable = 8P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   16 24
  8P LOSS WILD-TYPE 63 68
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               40               131 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               24                68 
$`8P LOSS MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABP TCGA-2L-AAQE 
       23.97         9.63         2.63        22.22        11.84        22.49 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IL TCGA-3A-A9IR 
       20.84         7.36        24.26        28.73        84.10        50.70 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-A7DR TCGA-FB-AAPU 
       34.09        12.39        10.98        17.00        11.61        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5926 TCGA-HZ-7289 TCGA-HZ-7919 
       23.54         5.03         1.02        17.79        21.73        19.50 
TCGA-HZ-7925 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-A8P1 TCGA-IB-7647 TCGA-IB-7890 
       20.19         3.95        17.92         0.23        21.90        19.66 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUQ TCGA-IB-AAUU TCGA-L1-A7W4 
        8.22        15.88         4.73         6.02         8.05         9.14 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-S4-A8RP TCGA-US-A776 
       12.46         8.78        23.08        27.75 

$`8P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI 
        2.17        20.61        19.96        22.72        22.26        31.86 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV 
       15.91        14.47        14.40        10.49         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 
        4.70         3.39        12.95         9.60        45.47        53.00 
TCGA-3A-A9I7 TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU 
       23.61        60.95        68.52        63.85        30.64        15.06 
TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6880 TCGA-F2-7273 
       31.79        10.13        75.12        71.74         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A545 
        7.10         7.66        19.27         3.12         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPY 
       14.76        12.43        15.95        37.15         7.50        34.82 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
       15.55         4.04         8.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       36.20        20.35        15.78        12.89        13.84        22.06 
TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
        0.92         7.76         0.13         0.26        27.62        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         9.83        12.43        14.93 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85         1.08        12.95        49.38         4.77 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       15.35        19.82        23.80        15.65        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
        3.62        43.79        15.81        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP 
       20.88        21.90         1.35         0.26         7.86        14.17 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A7SX 
       11.11         7.40         9.44        13.28         7.56        12.92 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       10.29        19.20        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A779 
        9.40         0.30        21.24        17.26        22.85        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       14.14         0.39        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.23              0.13 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            84.10             75.12 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            16.44             14.14 
[1] "0.2 - 84.1 (16.4)" "0.1 - 75.1 (14.1)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  8P LOSS MUTATED         1        2        4         9        22         1
  8P LOSS WILD-TYPE       0        4        9        17        95         4
                   vv
clus                STAGE IV
  8P LOSS MUTATED          1
  8P LOSS WILD-TYPE        3
D53V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                2                 4
  STAGE IB                4                 9
  STAGE IIA               9                17
  STAGE IIB              22                95
  STAGE III               1                 4
  STAGE IV                1                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P LOSS MUTATED     3   6  31   0
  8P LOSS WILD-TYPE   5  15 108   4
D53V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                 5
  T2               6                15
  T3              31               108
  T4               0                 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"
D53V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    15  23
  8P LOSS WILD-TYPE  30 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     15   23
  8P LOSS WILD-TYPE   30  101
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              15                30
  1              23               101
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   18  1
  8P LOSS WILD-TYPE 62  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     18    1
  8P LOSS WILD-TYPE   62    3
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              18                62
  1               1                 3
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   16 24
  8P LOSS WILD-TYPE 62 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     16   24
  8P LOSS WILD-TYPE   62   71
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              16                62
  MALE                24                71
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8P LOSS MUTATED                                    32
  8P LOSS WILD-TYPE                                 113
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8P LOSS MUTATED                                       5
  8P LOSS WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  8P LOSS MUTATED                                                  2
  8P LOSS WILD-TYPE                                                2
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  8P LOSS MUTATED                                     1
  8P LOSS WILD-TYPE                                   0
D53V8, multiclass
                                                  clus
vv                                                 8P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           32
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 8P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            113
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D53V9, continuous
D53V10, continuous
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   28 10  1  1
  8P LOSS WILD-TYPE 80 41  1  3
D53V11, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              28                80
  R1              10                41
  R2               1                 1
  RX               1                 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"
D53V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       2                         1    36
  8P LOSS WILD-TYPE     1                         6   122
D53V13, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  36               122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0  31
  8P LOSS WILD-TYPE   3 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   31
  8P LOSS WILD-TYPE    3  104
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              31               104
[1] 2 2
[1] FALSE

Clustering(54) Variable = 8Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    7  9
  8Q LOSS WILD-TYPE 72 83
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               155 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9                83 
$`8Q LOSS MUTATED`
TCGA-2J-AAB8 TCGA-2L-AAQE TCGA-3A-A9IL TCGA-3A-A9J0 TCGA-FB-A7DR TCGA-FB-AAPZ 
        2.63        22.49        84.10        12.39        11.61        23.54 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-HZ-7289 TCGA-HZ-8005 TCGA-IB-AAUN TCGA-IB-AAUQ 
        5.03         1.02        21.73         3.95         4.73         6.02 
TCGA-IB-AAUU TCGA-LB-A8F3 TCGA-S4-A8RP TCGA-US-A776 
        8.05        12.46        23.08        27.75 

$`8Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.72        22.26        31.86        15.91        14.47        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.40        10.49         9.11        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       12.95         9.60        45.47        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        24.26        28.73        60.95        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        30.64        15.06        31.79        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
        7.66        19.27         3.12        17.00         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       14.76        12.43        15.95        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
       34.82        15.55         4.04         8.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 
        5.10        36.20        20.35        15.78        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       13.84        22.06         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        0.69         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
       21.90        15.35        19.82        23.80        15.65        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS 
       15.88         0.26         7.86        14.17        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A9Q5 
        9.44        13.28         7.56         9.14        12.92        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A779 
        9.40         0.30        21.24        17.26        22.85        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       14.14         0.39        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.02              0.13 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            84.10             75.12 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            12.00             14.47 
[1] "1.0 - 84.1 (12.0)" "0.1 - 75.1 (14.5)"
[1] "hr=" "1.1"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  8Q LOSS MUTATED         1        0        1         3        11         0
  8Q LOSS WILD-TYPE       0        6       12        23       106         5
                   vv
clus                STAGE IV
  8Q LOSS MUTATED          0
  8Q LOSS WILD-TYPE        4
D54V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 6
  STAGE IB                1                12
  STAGE IIA               3                23
  STAGE IIB              11               106
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED     1   2  13   0
  8Q LOSS WILD-TYPE   7  19 126   4
D54V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1                 7
  T2               2                19
  T3              13               126
  T4               0                 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"
D54V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     3  11
  8Q LOSS WILD-TYPE  42 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3   11
  8Q LOSS WILD-TYPE   42  113
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               3                42
  1              11               113
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    6  0
  8Q LOSS WILD-TYPE 74  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6    0
  8Q LOSS WILD-TYPE   74    4
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               6                74
  1               0                 4
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    6 10
  8Q LOSS WILD-TYPE 72 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   10
  8Q LOSS WILD-TYPE   72   85
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               6                72
  MALE                10                85
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8Q LOSS MUTATED                                    12
  8Q LOSS WILD-TYPE                                 133
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8Q LOSS MUTATED                                       2
  8Q LOSS WILD-TYPE                                    20
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  8Q LOSS MUTATED                                                  2
  8Q LOSS WILD-TYPE                                                2
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  8Q LOSS MUTATED                                     0
  8Q LOSS WILD-TYPE                                   1
D54V8, multiclass
                                                  clus
vv                                                 8Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 8Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            133
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           20
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D54V9, continuous
D54V10, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                43 
       TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IJ        TCGA-3A-A9IR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUV        TCGA-LB-A7SX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-US-A774 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-YY-A8LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  8Q LOSS MUTATED   10  5  0  1
  8Q LOSS WILD-TYPE 98 46  2  3
D54V11, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              10                98
  R1               5                46
  R2               0                 2
  RX               1                 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"
D54V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       1                         1    14
  8Q LOSS WILD-TYPE     2                         6   144
D54V13, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  14               144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  13
  8Q LOSS WILD-TYPE   3 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   13
  8Q LOSS WILD-TYPE    3  122
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              13               122
[1] 2 2
[1] FALSE

Clustering(55) Variable = 9P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   26 44
  9P LOSS WILD-TYPE 53 48
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               70               101 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               44                48 
$`9P LOSS MUTATED`
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABO 
       19.96        22.22        22.72        22.26        31.86        14.47 
TCGA-2J-AABT TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I9 
       10.49        22.49         3.39        12.95         9.60        20.84 
TCGA-3A-A9IB TCGA-3A-A9IU TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
        7.36        15.06        12.39        71.74        10.98         7.66 
TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       19.27        17.00        24.07        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       34.82        15.55         4.04         5.03         1.02         8.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5924 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        15.78        17.79 
TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-7925 
       12.89        22.06        21.73         0.92         0.13        20.19 
TCGA-HZ-8005 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7645 
        3.95        21.70         6.38        21.60         5.26        49.38 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       21.90        15.35        23.80        41.33         4.04         3.62 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7LX TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX 
       17.16        15.85         8.22         8.05         9.14        12.92 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-RB-AA9M TCGA-S4-A8RP TCGA-US-A779 
       12.46         8.78        15.45         9.40        23.08        16.80 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        13.32        12.76        66.28 

$`9P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABK 
        2.17        23.97         9.63         2.63        20.61        15.91 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQM 
       11.84        14.40         9.11        21.44         4.70        45.47 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       53.00        23.61        24.26        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        63.85        50.70        30.64        31.79        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A7TX 
       10.13        75.12         9.70        19.46         7.10         3.12 
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPZ 
        5.88        14.76        12.43        11.61        15.95        23.54 
TCGA-FZ-5923 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 
       20.35        13.84        19.50         7.76         0.26        27.62 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A77P 
       14.93        17.92         4.96        16.14        10.13        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-7654 
        1.08         0.23        12.95         4.77        19.82        15.65 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
        2.47        12.00         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         9.44        13.28         7.56 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS 
       10.29        19.20        13.68         3.12        15.32         0.30 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G 
       21.24        17.26        22.85        27.75        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-YB-A89D TCGA-Z5-AAPL 
       18.67        13.81        12.99        11.51         0.69 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.23 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            71.74             84.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           14.765            14.140 
[1] "0.1 - 71.7 (14.8)" "0.2 - 84.1 (14.1)"
[1] "hr=" "1.3"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  9P LOSS MUTATED         0        1        0        15        52         3
  9P LOSS WILD-TYPE       1        5       13        11        65         2
                   vv
clus                STAGE IV
  9P LOSS MUTATED          0
  9P LOSS WILD-TYPE        4
D55V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 5
  STAGE IB                0                13
  STAGE IIA              15                11
  STAGE IIB              52                65
  STAGE III               3                 2
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED    2  4 64  1
  9P LOSS WILD-TYPE  6 17 75  3
D55V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               2                 6
  T2               4                17
  T3              64                75
  T4               1                 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"
D55V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   17 54
  9P LOSS WILD-TYPE 28 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     17   54
  9P LOSS WILD-TYPE   28   70
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              17                28
  1              54                70
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   32  0
  9P LOSS WILD-TYPE 48  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     32    0
  9P LOSS WILD-TYPE   48    4
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              32                48
  1               0                 4
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   32 39
  9P LOSS WILD-TYPE 46 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     32   39
  9P LOSS WILD-TYPE   46   56
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              32                46
  MALE                39                56
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9P LOSS MUTATED                                    64
  9P LOSS WILD-TYPE                                  81
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9P LOSS MUTATED                                       6
  9P LOSS WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  9P LOSS MUTATED                                                  0
  9P LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  9P LOSS MUTATED                                     0
  9P LOSS WILD-TYPE                                   1
D55V8, multiclass
                                                  clus
vv                                                 9P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           64
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 9P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             81
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D55V9, continuous
D55V10, continuous
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED   40 22  1  2
  9P LOSS WILD-TYPE 68 29  1  2
D55V11, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              40                68
  R1              22                29
  R2               1                 1
  RX               2                 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"
D55V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       2                         3    63
  9P LOSS WILD-TYPE     1                         4    95
D55V13, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  63                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    2 51
  9P LOSS WILD-TYPE  1 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   51
  9P LOSS WILD-TYPE    1   84
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              51                84
[1] 2 2
[1] FALSE

Clustering(56) Variable = 9Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   18 23
  9Q LOSS WILD-TYPE 61 69
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               41               130 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23                69 
$`9Q LOSS MUTATED`
TCGA-2J-AABF TCGA-2J-AABO TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9IB 
       22.72        14.47        22.49         3.39        12.95         7.36 
TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-AAPS TCGA-FB-AAPY 
       12.39        71.74         7.66        19.27         7.50        34.82 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 
       15.55         4.04         8.02        24.36         5.10        36.20 
TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7922 
       15.78        17.79        12.89        22.06         0.92         0.13 
TCGA-HZ-8005 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7645 
        3.95        21.70         6.38        21.60         5.26        49.38 
TCGA-IB-7649 TCGA-IB-A7LX TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-PZ-A5RE 
       15.35         8.22         8.05        12.92        12.46        15.45 
TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH 
        3.12         9.40        13.32        12.76        66.28 

$`9Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR 
       22.22        22.26        31.86        15.91        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQL TCGA-2L-AAQM 
       10.49         9.11        21.44         4.70         9.60        45.47 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       53.00        23.61        20.84        24.26        28.73        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       84.10        68.52        63.85        50.70        30.64        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 
       31.79        34.09        10.13        75.12        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 
       19.46         7.10         3.12        17.00         5.88        24.07 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       14.76        12.43        11.61        15.95        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5920 TCGA-FZ-5923 TCGA-H6-A45N 
       23.54         5.03         1.02         2.01        20.35        13.84 
TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
       21.73        19.50         7.76         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        12.03         0.69         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A77P 
       14.93        17.92         4.96        16.14        10.13        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 
        1.08         0.23        12.95         4.77        21.90        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       23.80        15.65        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         9.44        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY 
        7.56         9.14        10.29        19.20         8.78        13.68 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         0.30        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       27.75        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-YB-A89D TCGA-Z5-AAPL 
       12.99        12.03        11.51         0.69 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.23 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            71.74             84.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           12.920            14.845 
[1] "0.1 - 71.7 (12.9)" "0.2 - 84.1 (14.8)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  9Q LOSS MUTATED         0        1        1         7        30         3
  9Q LOSS WILD-TYPE       1        5       12        19        87         2
                   vv
clus                STAGE IV
  9Q LOSS MUTATED          0
  9Q LOSS WILD-TYPE        4
D56V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 5
  STAGE IB                1                12
  STAGE IIA               7                19
  STAGE IIB              30                87
  STAGE III               3                 2
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED     2   4  35   1
  9Q LOSS WILD-TYPE   6  17 104   3
D56V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               2                 6
  T2               4                17
  T3              35               104
  T4               1                 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"
D56V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    9 33
  9Q LOSS WILD-TYPE 36 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9   33
  9Q LOSS WILD-TYPE   36   91
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               9                36
  1              33                91
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   14  0
  9Q LOSS WILD-TYPE 66  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     14    0
  9Q LOSS WILD-TYPE   66    4
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              14                66
  1               0                 4
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   20 22
  9Q LOSS WILD-TYPE 58 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     20   22
  9Q LOSS WILD-TYPE   58   73
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              20                58
  MALE                22                73
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9Q LOSS MUTATED                                    39
  9Q LOSS WILD-TYPE                                 106
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9Q LOSS MUTATED                                       2
  9Q LOSS WILD-TYPE                                    20
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  9Q LOSS MUTATED                                                  0
  9Q LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  9Q LOSS MUTATED                                     0
  9Q LOSS WILD-TYPE                                   1
D56V8, multiclass
                                                  clus
vv                                                 9Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           39
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 9Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            106
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           20
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D56V9, continuous
D56V10, continuous
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED   25 11  0  1
  9Q LOSS WILD-TYPE 83 40  2  3
D56V11, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              25                83
  R1              11                40
  R2               0                 2
  RX               1                 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"
D56V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         2    37
  9Q LOSS WILD-TYPE     3                         5   121
D56V13, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  37               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  31
  9Q LOSS WILD-TYPE   1 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   31
  9Q LOSS WILD-TYPE    1  104
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              31               104
[1] 2 2
[1] FALSE

Clustering(57) Variable = 10P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   12 21
  10P LOSS WILD-TYPE 67 71
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                33                138 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                21                 71 
$`10P LOSS MUTATED`
TCGA-2J-AABA TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQI 
       19.96        31.86        14.47        11.84         9.11         3.39 
TCGA-2L-AAQM TCGA-3A-A9IC TCGA-3A-A9IL TCGA-3A-A9IS TCGA-3A-A9IU TCGA-FB-A545 
       45.47        24.26        84.10        30.64        15.06        24.07 
TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-H6-8124 
       15.95        23.54         5.03         5.10        20.35        12.89 
TCGA-HZ-7289 TCGA-HZ-8005 TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7646 TCGA-IB-7885 
       21.73         3.95         5.26         1.08         4.77        41.33 
TCGA-IB-7886 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-A5SQ TCGA-IB-A6UG TCGA-IB-A7LX 
        4.04        19.66         3.85         7.20         1.35         8.22 
TCGA-IB-AAUN TCGA-S4-A8RO TCGA-XD-AAUG 
        4.73        17.26        13.81 

$`10P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABV 
       22.72        22.26        15.91        14.40        10.49        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
        4.70        22.49        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
       20.84         7.36        28.73        60.95        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       50.70        31.79        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T 
       19.27         3.12        17.00         5.88        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ0 
       11.61        37.15         7.50        12.53        34.82        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 
        4.04         1.02         8.02        24.36         2.01        36.20 
TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 
       15.78        17.79        13.84        22.06         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
        7.76         0.13         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03         0.69         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       17.92         4.96        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
       21.60        10.85         0.23        12.95        49.38        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7887 TCGA-IB-7888 
       15.35        19.82        23.80        15.65         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       15.81        21.30        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.85        15.12        20.88        21.90        15.88         0.26 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        8.05        13.28         7.56         9.14        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40         0.30        21.24        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH 
       27.75        16.80        14.14         0.39        18.67        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.08               0.13 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             84.10              75.12 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            13.810             14.285 
[1] "1.1 - 84.1 (13.8)" "0.1 - 75.1 (14.3)"
[1] "hr=" "1.3"
D57V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  10P LOSS MUTATED         1        0        4         2        25         0
  10P LOSS WILD-TYPE       0        6        9        24        92         5
                    vv
clus                 STAGE IV
  10P LOSS MUTATED          2
  10P LOSS WILD-TYPE        2
D57V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  6
  STAGE IB                 4                  9
  STAGE IIA                2                 24
  STAGE IIB               25                 92
  STAGE III                0                  5
  STAGE IV                 2                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED     1   6  26   1
  10P LOSS WILD-TYPE   7  15 113   3
D57V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                1                  7
  T2                6                 15
  T3               26                113
  T4                1                  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"
D57V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    6 27
  10P LOSS WILD-TYPE 39 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6   27
  10P LOSS WILD-TYPE   39   97
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                6                 39
  1               27                 97
[1] 2 2
[1] FALSE
D57V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   16  2
  10P LOSS WILD-TYPE 64  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     16    2
  10P LOSS WILD-TYPE   64    2
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               16                 64
  1                2                  2
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   15 19
  10P LOSS WILD-TYPE 63 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     15   19
  10P LOSS WILD-TYPE   63   76
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               15                 63
  MALE                 19                 76
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10P LOSS MUTATED                                    27
  10P LOSS WILD-TYPE                                 118
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10P LOSS MUTATED                                       6
  10P LOSS WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  10P LOSS MUTATED                                                  0
  10P LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  10P LOSS MUTATED                                     1
  10P LOSS WILD-TYPE                                   0
D57V8, multiclass
                                                  clus
vv                                                 10P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            27
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 10P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D57V9, continuous
D57V10, continuous
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED   21 10  0  1
  10P LOSS WILD-TYPE 87 41  2  3
D57V11, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               21                 87
  R1               10                 41
  R2                0                  2
  RX                1                  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"
D57V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         0    32
  10P LOSS WILD-TYPE     3                         7   126
D57V13, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   32                126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     0  25
  10P LOSS WILD-TYPE   3 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0   25
  10P LOSS WILD-TYPE    3  110
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               25                110
[1] 2 2
[1] FALSE

Clustering(58) Variable = 10Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   12 15
  10Q LOSS WILD-TYPE 67 77
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                27                144 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                 77 
$`10Q LOSS MUTATED`
TCGA-2J-AABA TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQI TCGA-2L-AAQM 
       19.96        14.47        11.84         9.11         3.39        45.47 
TCGA-3A-A9IL TCGA-3A-A9IS TCGA-3A-A9IU TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAQ2 
       84.10        30.64        15.06        24.07        15.95         5.03 
TCGA-FZ-5921 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-8005 TCGA-HZ-A77O 
        5.10        12.89        21.73         0.92         3.95         5.26 
TCGA-HZ-A77Q TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 
        1.08         4.77        41.33         3.62        19.66         3.85 
TCGA-S4-A8RO TCGA-US-A776 TCGA-XD-AAUG 
       17.26        27.75        13.81 

$`10Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABT 
       22.72        22.26        31.86        15.91        14.40        10.49 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
       21.44         4.70        22.49        12.95         9.60        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       23.61        20.84         7.36        24.26        28.73        60.95 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       68.52        63.85        50.70        31.79        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       12.39        75.12        71.74        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
        7.10         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       14.76        12.43        11.61        37.15         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       34.82        23.54        15.55         4.04         1.02         8.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 
       24.36         2.01        36.20        20.35        15.78        17.79 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       13.84        22.06        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A8P1 
       16.14        10.13         6.38        21.60        10.85         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       12.95        49.38        21.90        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 
       15.65         4.04        43.79        15.81        21.30        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX 
        9.44         8.05        13.28         7.56         9.14        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RP 
        3.12        15.32         9.40         0.30        21.24        23.08 
TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH 
       22.85        16.80        14.14         0.39        18.67        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.92               0.13 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             84.10              75.12 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            13.810             14.285 
[1] "0.9 - 84.1 (13.8)" "0.1 - 75.1 (14.3)"
[1] "hr=" "1.1"
D58V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  10Q LOSS MUTATED         1        0        2         2        21         0
  10Q LOSS WILD-TYPE       0        6       11        24        96         5
                    vv
clus                 STAGE IV
  10Q LOSS MUTATED          1
  10Q LOSS WILD-TYPE        3
D58V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  6
  STAGE IB                 2                 11
  STAGE IIA                2                 24
  STAGE IIB               21                 96
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED     1   3  23   0
  10Q LOSS WILD-TYPE   7  18 116   4
D58V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                1                  7
  T2                3                 18
  T3               23                116
  T4                0                  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"
D58V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4  22
  10Q LOSS WILD-TYPE  41 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4   22
  10Q LOSS WILD-TYPE   41  102
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                4                 41
  1               22                102
[1] 2 2
[1] FALSE
D58V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   13  1
  10Q LOSS WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     13    1
  10Q LOSS WILD-TYPE   67    3
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               13                 67
  1                1                  3
[1] 2 2
[1] FALSE
D58V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   12 15
  10Q LOSS WILD-TYPE 66 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     12   15
  10Q LOSS WILD-TYPE   66   80
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               12                 66
  MALE                 15                 80
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10Q LOSS MUTATED                                    20
  10Q LOSS WILD-TYPE                                 125
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10Q LOSS MUTATED                                       5
  10Q LOSS WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  10Q LOSS MUTATED                                                  1
  10Q LOSS WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  10Q LOSS MUTATED                                     1
  10Q LOSS WILD-TYPE                                   0
D58V8, multiclass
                                                  clus
vv                                                 10Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            20
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 10Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D58V9, continuous
D58V10, continuous
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED   16  8  0  1
  10Q LOSS WILD-TYPE 92 43  2  3
D58V11, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               16                 92
  R1                8                 43
  R2                0                  2
  RX                1                  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"
D58V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         0    25
  10Q LOSS WILD-TYPE     3                         7   133
D58V13, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   25                133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     0  19
  10Q LOSS WILD-TYPE   3 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0   19
  10Q LOSS WILD-TYPE    3  116
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               19                116
[1] 2 2
[1] FALSE

Clustering(59) Variable = 11P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    9  6
  11P LOSS WILD-TYPE 70 86
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                156 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 86 
$`11P LOSS MUTATED`
TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IS TCGA-3A-A9J0 TCGA-F2-A44H TCGA-FB-AAPP 
       45.47        84.10        30.64        12.39        19.27        15.95 
TCGA-FB-AAPZ TCGA-FZ-5924 TCGA-HZ-7918 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7889 
       23.54        15.78         0.92        23.80         4.04        15.81 
TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUI 
       12.92        17.26        12.03 

$`11P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
       22.49         3.39        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN 
       20.84         7.36        24.26        28.73        60.95        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        15.06        31.79        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
        7.66         3.12        17.00         5.88        24.07        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       12.43        11.61        37.15         7.50        12.53        34.82 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       15.55         4.04         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H6-8124 
        2.01         5.10        36.20        20.35        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       13.84        22.06        21.73        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        15.65        41.33 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
        3.62        43.79        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 
        9.44         8.05        13.28         7.56         9.14        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40         0.30        21.24        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       27.75        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.99        13.32        11.51        12.76        66.28         0.69 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.92               0.13 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             84.10              75.12 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            15.950             13.825 
[1] "0.9 - 84.1 (15.9)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.8"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  11P LOSS MUTATED         1        0        1         1        12         0
  11P LOSS WILD-TYPE       0        6       12        25       105         5
                    vv
clus                 STAGE IV
  11P LOSS MUTATED          0
  11P LOSS WILD-TYPE        4
D59V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  6
  STAGE IB                 1                 12
  STAGE IIA                1                 25
  STAGE IIB               12                105
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED     1   2  12   0
  11P LOSS WILD-TYPE   7  19 127   4
D59V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                  7
  T2                2                 19
  T3               12                127
  T4                0                  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"
D59V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  12
  11P LOSS WILD-TYPE  43 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   12
  11P LOSS WILD-TYPE   43  112
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                2                 43
  1               12                112
[1] 2 2
[1] FALSE
D59V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    6  0
  11P LOSS WILD-TYPE 74  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    0
  11P LOSS WILD-TYPE   74    4
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                6                 74
  1                0                  4
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    6  9
  11P LOSS WILD-TYPE 72 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    9
  11P LOSS WILD-TYPE   72   86
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                6                 72
  MALE                  9                 86
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11P LOSS MUTATED                                    12
  11P LOSS WILD-TYPE                                 133
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11P LOSS MUTATED                                       3
  11P LOSS WILD-TYPE                                    19
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  11P LOSS MUTATED                                                  0
  11P LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  11P LOSS MUTATED                                     0
  11P LOSS WILD-TYPE                                   1
D59V8, multiclass
                                                  clus
vv                                                 11P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 11P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             133
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D59V9, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 52 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABI         TCGA-2J-AABO 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-2J-AABV         TCGA-2L-AAQA         TCGA-2L-AAQE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-3A-A9I9         TCGA-3A-A9IB         TCGA-3A-A9IJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-6880         TCGA-F2-A8YN 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H6-A45N 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7887 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A6UG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUU         TCGA-IB-AAUV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-XD-AAUL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-YY-A8LH 
"11P LOSS WILD-TYPE" 
D59V10, continuous
                    vv
clus                 R0 R1 R2 RX
  11P LOSS MUTATED    9  6  0  0
  11P LOSS WILD-TYPE 99 45  2  4
D59V11, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                9                 99
  R1                6                 45
  R2                0                  2
  RX                0                  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"
D59V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         1    13
  11P LOSS WILD-TYPE     2                         6   145
D59V13, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   13                145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  14
  11P LOSS WILD-TYPE   3 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   14
  11P LOSS WILD-TYPE    3  121
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               14                121
[1] 2 2
[1] FALSE

Clustering(60) Variable = 11Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    9  5
  11Q LOSS WILD-TYPE 70 87
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                14                157 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 87 
$`11Q LOSS MUTATED`
TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IS TCGA-3A-A9J0 TCGA-F2-A44H TCGA-FB-A78T 
       45.47        84.10        30.64        12.39        19.27        12.43 
TCGA-FB-AAPP TCGA-FZ-5924 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-A77P TCGA-LB-A7SX 
       15.95        15.78        21.73         0.92        10.85        12.92 
TCGA-US-A776 TCGA-XD-AAUI 
       27.75        12.03 

$`11Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 
       22.49         3.39        12.95         9.60        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN 
       20.84         7.36        24.26        28.73        60.95        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        15.06        31.79        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
        7.66         3.12        17.00         5.88        24.07        14.76 
TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       11.61        37.15         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       15.55         4.04         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H6-8124 
        2.01         5.10        36.20        20.35        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       13.84        22.06        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        3.95         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       15.35        19.82        23.80        15.65        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
        3.62        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.98         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.12        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO 
        3.12        15.32         9.40         0.30        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       23.08        22.85        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       13.81        12.99        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.92               0.13 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             84.10              75.12 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            15.865             14.140 
[1] "0.9 - 84.1 (15.9)" "0.1 - 75.1 (14.1)"
[1] "hr=" "2.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  11Q LOSS MUTATED         1        0        1         2        10         0
  11Q LOSS WILD-TYPE       0        6       12        24       107         5
                    vv
clus                 STAGE IV
  11Q LOSS MUTATED          0
  11Q LOSS WILD-TYPE        4
D60V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  6
  STAGE IB                 1                 12
  STAGE IIA                2                 24
  STAGE IIB               10                107
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED     1   1  12   0
  11Q LOSS WILD-TYPE   7  20 127   4
D60V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                  7
  T2                1                 20
  T3               12                127
  T4                0                  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"
D60V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  10
  11Q LOSS WILD-TYPE  42 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   10
  11Q LOSS WILD-TYPE   42  114
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                3                 42
  1               10                114
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    4  0
  11Q LOSS WILD-TYPE 76  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4    0
  11Q LOSS WILD-TYPE   76    4
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                4                 76
  1                0                  4
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    4 10
  11Q LOSS WILD-TYPE 74 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4   10
  11Q LOSS WILD-TYPE   74   85
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                4                 74
  MALE                 10                 85
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11Q LOSS MUTATED                                     8
  11Q LOSS WILD-TYPE                                 137
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11Q LOSS MUTATED                                       5
  11Q LOSS WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  11Q LOSS MUTATED                                                  1
  11Q LOSS WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  11Q LOSS MUTATED                                     0
  11Q LOSS WILD-TYPE                                   1
D60V8, multiclass
                                                  clus
vv                                                 11Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 11Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             137
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D60V9, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 52 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABI         TCGA-2J-AABO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-2J-AABV         TCGA-2L-AAQA         TCGA-2L-AAQE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-3A-A9I9         TCGA-3A-A9IB         TCGA-3A-A9IJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-6880         TCGA-F2-A8YN 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A7DR 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-FB-AAPY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-H6-8124         TCGA-H6-A45N         TCGA-H8-A6C1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A6UG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUU         TCGA-IB-AAUV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-XD-AAUL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-YY-A8LH 
"11Q LOSS WILD-TYPE" 
D60V10, continuous
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED   10  3  0  1
  11Q LOSS WILD-TYPE 98 48  2  3
D60V11, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               10                 98
  R1                3                 48
  R2                0                  2
  RX                1                  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"
D60V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       0                         1    13
  11Q LOSS WILD-TYPE     3                         6   145
D60V13, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   13                145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  13
  11Q LOSS WILD-TYPE   3 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   13
  11Q LOSS WILD-TYPE    3  122
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               13                122
[1] 2 2
[1] FALSE

Clustering(61) Variable = 12P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    8 10
  12P LOSS WILD-TYPE 71 82
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                18                153 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                10                 82 
$`12P LOSS MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABP TCGA-2L-AAQE TCGA-3A-A9IC TCGA-3A-A9IH 
       23.97         2.63        11.84        22.49        24.26        28.73 
TCGA-3A-A9J0 TCGA-F2-A8YN TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FZ-5920 TCGA-HZ-7919 
       12.39        17.00        11.61        37.15         2.01        19.50 
TCGA-HZ-8636 TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-A5SP TCGA-IB-AAUU TCGA-LB-A7SX 
       17.92         4.04         3.85        15.85         8.05        12.92 

$`12P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF 
        2.17         9.63        20.61        19.96        22.22        22.72 
TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABT 
       22.26        31.86        15.91        14.47        14.40        10.49 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IJ 
       45.47        53.00        23.61        20.84         7.36        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       84.10        68.52        63.85        50.70        30.64        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       31.79        34.09        10.13        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.70        19.46         7.10         7.66        19.27         3.12 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS 
        5.88        24.07        14.76        12.43        15.95         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02         8.02        24.36         5.10        36.20        20.35 
TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
       15.78        17.79        12.89        13.84        22.06        21.73 
TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
        0.92         7.76         0.13         0.26        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03         0.69         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       12.95        49.38         4.77        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       23.80        15.65        41.33         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       19.66        21.30        15.98         2.47        17.16        12.00 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
       11.11         7.40         9.44        13.28         7.56         9.14 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.46        10.29        19.20         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO 
        3.12        15.32         9.40         0.30        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              2.01               0.13 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             37.15              84.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            14.385             14.170 
[1] "2.0 - 37.1 (14.4)" "0.1 - 84.1 (14.2)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  12P LOSS MUTATED         0        1        0         4        12         0
  12P LOSS WILD-TYPE       1        5       13        22       105         5
                    vv
clus                 STAGE IV
  12P LOSS MUTATED          1
  12P LOSS WILD-TYPE        3
D61V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  5
  STAGE IB                 0                 13
  STAGE IIA                4                 22
  STAGE IIB               12                105
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED     1   1  16   0
  12P LOSS WILD-TYPE   7  20 123   4
D61V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                  7
  T2                1                 20
  T3               16                123
  T4                0                  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"
D61V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  12
  12P LOSS WILD-TYPE  40 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   12
  12P LOSS WILD-TYPE   40  112
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                5                 40
  1               12                112
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   12  1
  12P LOSS WILD-TYPE 68  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12    1
  12P LOSS WILD-TYPE   68    3
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               12                 68
  1                1                  3
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    6 12
  12P LOSS WILD-TYPE 72 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6   12
  12P LOSS WILD-TYPE   72   83
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                6                 72
  MALE                 12                 83
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12P LOSS MUTATED                                    15
  12P LOSS WILD-TYPE                                 130
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12P LOSS MUTATED                                       1
  12P LOSS WILD-TYPE                                    21
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  12P LOSS MUTATED                                                  1
  12P LOSS WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  12P LOSS MUTATED                                     1
  12P LOSS WILD-TYPE                                   0
D61V8, multiclass
                                                  clus
vv                                                 12P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 12P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             130
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D61V9, continuous
D61V10, continuous
                    vv
clus                 R0 R1 R2 RX
  12P LOSS MUTATED   11  7  0  0
  12P LOSS WILD-TYPE 97 44  2  4
D61V11, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               11                 97
  R1                7                 44
  R2                0                  2
  RX                0                  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"
D61V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       1                         2    15
  12P LOSS WILD-TYPE     2                         5   143
D61V13, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   15                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  13
  12P LOSS WILD-TYPE   3 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   13
  12P LOSS WILD-TYPE    3  122
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               13                122
[1] 2 2
[1] FALSE

Clustering(62) Variable = 12Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    9 15
  12Q LOSS WILD-TYPE 70 77
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                24                147 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                 77 
$`12Q LOSS MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABH TCGA-2J-AABI TCGA-2L-AAQE TCGA-2L-AAQI 
       23.97         2.63        22.26        31.86        22.49         3.39 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9J0 TCGA-FB-A7DR TCGA-FB-AAQ2 TCGA-FZ-5920 
       24.26        28.73        12.39        11.61         5.03         2.01 
TCGA-FZ-5924 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 
       15.78        17.92         5.26        23.80         4.04         3.62 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-AAUN TCGA-IB-AAUU TCGA-LB-A7SX TCGA-YH-A8SY 
       19.66         3.85         4.73         8.05        12.92        12.76 

$`12Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF 
        2.17         9.63        20.61        19.96        22.22        22.72 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU 
       15.91        14.47        11.84        14.40        10.49         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 
       21.44         4.70        12.95         9.60        45.47        53.00 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
       23.61        20.84         7.36        60.95        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       10.13        75.12        71.74        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 
        7.10         7.66        19.27         3.12        17.00         5.88 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       24.07        14.76        12.43        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 
       12.53        34.82        23.54        15.55         4.04         1.02 
TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        8.02        24.36         5.10        36.20        20.35        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       12.89        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
        7.76         0.13         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       14.93         4.96        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
       21.60        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        15.65        41.33 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       43.79        15.81        21.30        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22        15.88         0.26         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         9.44        13.28         7.56 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        9.14        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       13.68         3.12        15.32         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        66.28         0.69 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              2.01               0.13 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             31.86              84.10 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            12.575             14.470 
[1] "2.0 - 31.9 (12.6)" "0.1 - 84.1 (14.5)"
[1] "hr=" "1.4"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  12Q LOSS MUTATED         0        1        2         4        15         1
  12Q LOSS WILD-TYPE       1        5       11        22       102         4
                    vv
clus                 STAGE IV
  12Q LOSS MUTATED          1
  12Q LOSS WILD-TYPE        3
D62V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  5
  STAGE IB                 2                 11
  STAGE IIA                4                 22
  STAGE IIB               15                102
  STAGE III                1                  4
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED     1   4  19   0
  12Q LOSS WILD-TYPE   7  17 120   4
D62V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                  7
  T2                4                 17
  T3               19                120
  T4                0                  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"
D62V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     7  16
  12Q LOSS WILD-TYPE  38 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      7   16
  12Q LOSS WILD-TYPE   38  108
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                7                 38
  1               16                108
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   15  1
  12Q LOSS WILD-TYPE 65  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     15    1
  12Q LOSS WILD-TYPE   65    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               15                 65
  1                1                  3
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   11 13
  12Q LOSS WILD-TYPE 67 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     11   13
  12Q LOSS WILD-TYPE   67   82
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               11                 67
  MALE                 13                 82
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12Q LOSS MUTATED                                    19
  12Q LOSS WILD-TYPE                                 126
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12Q LOSS MUTATED                                       3
  12Q LOSS WILD-TYPE                                    19
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  12Q LOSS MUTATED                                                  1
  12Q LOSS WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  12Q LOSS MUTATED                                     0
  12Q LOSS WILD-TYPE                                   1
D62V8, multiclass
                                                  clus
vv                                                 12Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 12Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D62V9, continuous
D62V10, continuous
                    vv
clus                 R0 R1 R2 RX
  12Q LOSS MUTATED   14  9  0  0
  12Q LOSS WILD-TYPE 94 42  2  4
D62V11, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               14                 94
  R1                9                 42
  R2                0                  2
  RX                0                  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"
D62V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       2                         2    19
  12Q LOSS WILD-TYPE     1                         5   139
D62V13, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   19                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  17
  12Q LOSS WILD-TYPE   3 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   17
  12Q LOSS WILD-TYPE    3  118
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               17                118
[1] 2 2
[1] FALSE

Clustering(63) Variable = 13Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    6 14
  13Q LOSS WILD-TYPE 73 78
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                151 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                 78 
$`13Q LOSS MUTATED`
TCGA-2J-AABU TCGA-2L-AAQJ TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IR TCGA-3A-A9IZ 
        9.11        12.95         7.36        24.26        50.70        10.13 
TCGA-FB-AAPP TCGA-FZ-5920 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-8636 TCGA-HZ-A4BK 
       15.95         2.01        21.73         0.92        17.92        21.60 
TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A7M4 
        4.77        41.33         4.04        17.16        15.12        15.88 
TCGA-L1-A7W4 TCGA-LB-A7SX 
        9.14        12.92 

$`13Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       11.84        14.40        10.49        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39         9.60        45.47        53.00        23.61        20.84 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IS 
       28.73        60.95        84.10        68.52        63.85        30.64 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        31.79        34.09        12.39        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.70        19.46         7.10         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
        3.12        17.00         5.88        24.07        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       11.61        37.15         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       15.55         4.04         5.03         1.02         8.02        24.36 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 
        5.10        36.20        20.35        15.78        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       13.84        22.06        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       16.14        10.13         6.38         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
        0.23        12.95        49.38        21.90        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        15.65         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       21.30         3.85        15.98         2.47        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM 
        7.20        20.88        21.90         1.35         8.22         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        9.44         8.05        13.28         7.56        12.46        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        9.40         0.30        21.24        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       27.75        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.92               0.13 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              50.7               84.1 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            14.035             14.170 
[1] "0.9 - 50.7 (14.0)" "0.1 - 84.1 (14.2)"
[1] "hr=" "1.5"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  13Q LOSS MUTATED         0        0        1         0        17         1
  13Q LOSS WILD-TYPE       1        6       12        26       100         4
                    vv
clus                 STAGE IV
  13Q LOSS MUTATED          1
  13Q LOSS WILD-TYPE        3
D63V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 1                 12
  STAGE IIA                0                 26
  STAGE IIB               17                100
  STAGE III                1                  4
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED     0   1  18   1
  13Q LOSS WILD-TYPE   8  20 121   3
D63V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                0                  8
  T2                1                 20
  T3               18                121
  T4                1                  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"
D63V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     3  17
  13Q LOSS WILD-TYPE  42 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3   17
  13Q LOSS WILD-TYPE   42  107
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                3                 42
  1               17                107
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9  1
  13Q LOSS WILD-TYPE 71  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    1
  13Q LOSS WILD-TYPE   71    3
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                9                 71
  1                1                  3
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9 11
  13Q LOSS WILD-TYPE 69 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   11
  13Q LOSS WILD-TYPE   69   84
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                 69
  MALE                 11                 84
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  13Q LOSS MUTATED                                    17
  13Q LOSS WILD-TYPE                                 128
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  13Q LOSS MUTATED                                       3
  13Q LOSS WILD-TYPE                                    19
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  13Q LOSS MUTATED                                                  0
  13Q LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  13Q LOSS MUTATED                                     0
  13Q LOSS WILD-TYPE                                   1
D63V8, multiclass
                                                  clus
vv                                                 13Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            17
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 13Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D63V9, continuous
D63V10, continuous
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED   10  8  1  1
  13Q LOSS WILD-TYPE 98 43  1  3
D63V11, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               10                 98
  R1                8                 43
  R2                1                  1
  RX                1                  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"
D63V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         2    18
  13Q LOSS WILD-TYPE     3                         5   140
D63V13, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   18                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  17
  13Q LOSS WILD-TYPE   2 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   17
  13Q LOSS WILD-TYPE    2  118
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               17                118
[1] 2 2
[1] FALSE

Clustering(64) Variable = 14Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    6  8
  14Q LOSS WILD-TYPE 73 84
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                14                157 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 8                 84 
$`14Q LOSS MUTATED`
TCGA-2J-AABA TCGA-2J-AABI TCGA-2L-AAQL TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9J0 
       19.96        31.86         9.60        24.26        28.73        12.39 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-HZ-8005 TCGA-IB-7647 TCGA-IB-AAUN TCGA-LB-A7SX 
       14.76        11.61         3.95        21.90         4.73        12.92 
TCGA-LB-A8F3 TCGA-YH-A8SY 
       12.46        12.76 

$`14Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABR 
       22.72        22.26        15.91        14.47        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95        45.47        53.00        23.61        20.84         7.36 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        84.10        68.52        63.85        50.70        30.64 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        31.79        34.09        10.13        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.70        19.46         7.10         7.66        19.27 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPP 
        3.12        17.00         5.88        24.07        12.43        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       37.15         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
        4.04         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 
        5.10        36.20        20.35        15.78        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       13.84        22.06        21.73         0.92        19.50         7.76 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
        0.13         0.26        27.62        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         0.69         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 
        4.77        15.35        19.82        23.80        15.65        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        27.75        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YY-A8LH 
       13.81        12.99        12.03        13.32        11.51        66.28 
TCGA-Z5-AAPL 
        0.69 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              3.95               0.13 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             31.86              84.10 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             12.84              14.40 
[1] "4.0 - 31.9 (12.8)" "0.1 - 84.1 (14.4)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  14Q LOSS MUTATED         0        1        2         3         7         1
  14Q LOSS WILD-TYPE       1        5       11        23       110         4
                    vv
clus                 STAGE IV
  14Q LOSS MUTATED          0
  14Q LOSS WILD-TYPE        4
D64V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  5
  STAGE IB                 2                 11
  STAGE IIA                3                 23
  STAGE IIB                7                110
  STAGE III                1                  4
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED     1   2  11   0
  14Q LOSS WILD-TYPE   7  19 128   4
D64V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                1                  7
  T2                2                 19
  T3               11                128
  T4                0                  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"
D64V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     5   8
  14Q LOSS WILD-TYPE  40 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5    8
  14Q LOSS WILD-TYPE   40  116
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0                5                 40
  1                8                116
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    6  0
  14Q LOSS WILD-TYPE 74  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      6    0
  14Q LOSS WILD-TYPE   74    4
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0                6                 74
  1                0                  4
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    7  7
  14Q LOSS WILD-TYPE 71 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      7    7
  14Q LOSS WILD-TYPE   71   88
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                7                 71
  MALE                  7                 88
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  14Q LOSS MUTATED                                    11
  14Q LOSS WILD-TYPE                                 134
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  14Q LOSS MUTATED                                       1
  14Q LOSS WILD-TYPE                                    21
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  14Q LOSS MUTATED                                                  1
  14Q LOSS WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  14Q LOSS MUTATED                                     0
  14Q LOSS WILD-TYPE                                   1
D64V8, multiclass
                                                  clus
vv                                                 14Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 14Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             134
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D64V9, continuous
D64V10, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED     7   5   0   1
  14Q LOSS WILD-TYPE 101  46   2   3
D64V11, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0                7                101
  R1                5                 46
  R2                0                  2
  RX                1                  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"
D64V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       1                         2    11
  14Q LOSS WILD-TYPE     2                         5   147
D64V13, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   11                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     0  11
  14Q LOSS WILD-TYPE   3 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   11
  14Q LOSS WILD-TYPE    3  124
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               11                124
[1] 2 2
[1] FALSE

Clustering(65) Variable = 15Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   13 13
  15Q LOSS WILD-TYPE 66 79
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                26                145 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                13                 79 
$`15Q LOSS MUTATED`
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABP TCGA-2J-AABT TCGA-3A-A9IB TCGA-3A-A9IS 
       22.22        22.26        11.84        10.49         7.36        30.64 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A7DR TCGA-FB-AAPP 
       71.74        10.98        17.00        24.07        11.61        15.95 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-HZ-8005 TCGA-HZ-A4BK TCGA-IB-7644 
       23.54        15.55         5.03         3.95        21.60        12.95 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7M4 TCGA-M8-A5N4 
       19.66         3.85        17.16        15.85        15.88        19.20 
TCGA-XD-AAUI TCGA-YH-A8SY 
       12.03        12.76 

$`15Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABF TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABU 
       22.72        31.86        15.91        14.47        14.40         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        53.00        23.61        20.84        24.26        28.73 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU 
       60.95        84.10        68.52        63.85        50.70        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6880 
       31.79        34.09        10.13        12.39        75.12         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 
       19.46         7.10         7.66        19.27         3.12         5.88 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       14.76        12.43        37.15         7.50        12.53        34.82 
TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         1.02         8.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       22.06        21.73         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        0.69         9.83        12.43        14.93        17.92         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P 
       21.70        16.14        10.13         6.38         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        1.08         0.23        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       19.82        23.80        15.65        41.33         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
       43.79        15.81        21.30        15.98         2.47        12.00 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        7.20        15.12        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 
        7.40         9.44         8.05        13.28         7.56         9.14 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.92        12.46        10.29         8.78        15.45        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO 
        3.12        15.32         9.40         0.30        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        27.75        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL TCGA-YB-A89D TCGA-YY-A8LH 
       18.67        13.81        12.99        13.32        11.51        66.28 
TCGA-Z5-AAPL 
        0.69 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              3.85               0.13 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             71.74              84.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            15.865             13.840 
[1] "3.9 - 71.7 (15.9)" "0.1 - 84.1 (13.8)"
[1] "hr=" "1.2"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  15Q LOSS MUTATED         0        0        2         9        13         1
  15Q LOSS WILD-TYPE       1        6       11        17       104         4
                    vv
clus                 STAGE IV
  15Q LOSS MUTATED          1
  15Q LOSS WILD-TYPE        3
D65V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 2                 11
  STAGE IIA                9                 17
  STAGE IIB               13                104
  STAGE III                1                  4
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED     0   3  23   0
  15Q LOSS WILD-TYPE   8  18 116   4
D65V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                0                  8
  T2                3                 18
  T3               23                116
  T4                0                  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"
D65V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    10  15
  15Q LOSS WILD-TYPE  35 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     10   15
  15Q LOSS WILD-TYPE   35  109
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               10                 35
  1               15                109
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   13  1
  15Q LOSS WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     13    1
  15Q LOSS WILD-TYPE   67    3
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               13                 67
  1                1                  3
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    9 17
  15Q LOSS WILD-TYPE 69 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      9   17
  15Q LOSS WILD-TYPE   69   78
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                9                 69
  MALE                 17                 78
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  15Q LOSS MUTATED                                    19
  15Q LOSS WILD-TYPE                                 126
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  15Q LOSS MUTATED                                       4
  15Q LOSS WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  15Q LOSS MUTATED                                                  1
  15Q LOSS WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  15Q LOSS MUTATED                                     1
  15Q LOSS WILD-TYPE                                   0
D65V8, multiclass
                                                  clus
vv                                                 15Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 15Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D65V9, continuous
D65V10, continuous
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   14  9  0  0
  15Q LOSS WILD-TYPE 94 42  2  4
D65V11, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               14                 94
  R1                9                 42
  R2                0                  2
  RX                0                  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"
D65V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       1                         0    23
  15Q LOSS WILD-TYPE     2                         7   135
D65V13, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   23                135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  17
  15Q LOSS WILD-TYPE   2 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   17
  15Q LOSS WILD-TYPE    2  118
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               17                118
[1] 2 2
[1] FALSE

Clustering(66) Variable = 16P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    6  3
  16P LOSS WILD-TYPE 73 89
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                162 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 89 
$`16P LOSS MUTATED`
TCGA-2J-AABA TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IS TCGA-FB-A545 
       19.96        11.84        45.47        84.10        30.64        24.07 
TCGA-FB-AAPZ TCGA-HZ-A4BK TCGA-IB-A7LX 
       23.54        21.60         8.22 

$`16P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.72        22.26        31.86        15.91        14.47        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        53.00        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        28.73        60.95        68.52        63.85        50.70 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        31.79        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T 
       19.27         3.12        17.00         5.88        14.76        12.43 
TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.61        15.95        37.15         7.50        12.53        34.82 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       15.55         4.04         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 
        2.01         5.10        36.20        20.35        15.78        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       12.89        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
        7.76         0.13         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       14.93        17.92         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
        6.38         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       15.65        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
        6.02        11.11         7.40         9.44         8.05        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.56         9.14        12.92        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              8.22               0.13 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             84.10              75.12 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            23.540             13.825 
[1] "8.2 - 84.1 (23.5)" "0.1 - 75.1 (13.8)"
[1] "hr=" "3"  
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  16P LOSS MUTATED         1        0        1         0         7         0
  16P LOSS WILD-TYPE       0        6       12        26       110         5
                    vv
clus                 STAGE IV
  16P LOSS MUTATED          0
  16P LOSS WILD-TYPE        4
D66V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  6
  STAGE IB                 1                 12
  STAGE IIA                0                 26
  STAGE IIB                7                110
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     1   2   6   0
  16P LOSS WILD-TYPE   7  19 133   4
D66V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                1                  7
  T2                2                 19
  T3                6                133
  T4                0                  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"
D66V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1   7
  16P LOSS WILD-TYPE  44 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    7
  16P LOSS WILD-TYPE   44  117
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                1                 44
  1                7                117
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3  0
  16P LOSS WILD-TYPE 77  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    0
  16P LOSS WILD-TYPE   77    4
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                3                 77
  1                0                  4
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3  6
  16P LOSS WILD-TYPE 75 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    6
  16P LOSS WILD-TYPE   75   89
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 75
  MALE                  6                 89
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16P LOSS MUTATED                                     4
  16P LOSS WILD-TYPE                                 141
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16P LOSS MUTATED                                       4
  16P LOSS WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  16P LOSS MUTATED                                                  0
  16P LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  16P LOSS MUTATED                                     1
  16P LOSS WILD-TYPE                                   0
D66V8, multiclass
                                                  clus
vv                                                 16P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 16P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             141
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D66V9, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 53 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2J-AABI         TCGA-2J-AABO         TCGA-2J-AABV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IJ         TCGA-3A-A9IX 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F2-6880         TCGA-F2-A8YN         TCGA-FB-A4P5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-A7DR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-FB-AAPY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-H6-8124         TCGA-H6-A45N         TCGA-H8-A6C1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A6UG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUU         TCGA-IB-AAUV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-YY-A8LH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D66V10, continuous
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED     5   3   0   0
  16P LOSS WILD-TYPE 103  48   2   4
D66V11, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                5                103
  R1                3                 48
  R2                0                  2
  RX                0                  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"
D66V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         0     9
  16P LOSS WILD-TYPE     3                         7   149
D66V13, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    9                149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   6
  16P LOSS WILD-TYPE   3 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    6
  16P LOSS WILD-TYPE    3  129
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                6                129
[1] 2 2
[1] FALSE

Clustering(67) Variable = 16Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    4  6
  16Q LOSS WILD-TYPE 75 86
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                161 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                 86 
$`16Q LOSS MUTATED`
TCGA-2J-AABA TCGA-2J-AABP TCGA-2L-AAQE TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IC 
       19.96        11.84        22.49         9.60        45.47        24.26 
TCGA-3A-A9IL TCGA-3A-A9IS TCGA-HZ-7289 TCGA-IB-A7LX 
       84.10        30.64        21.73         8.22 

$`16Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       22.72        22.26        31.86        15.91        14.47        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ 
       10.49         9.11        21.44         4.70         3.39        12.95 
TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IJ 
       53.00        23.61        20.84         7.36        28.73        60.95 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        63.85        50.70        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP 
        5.88        24.07        14.76        12.43        11.61        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       37.15         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
        4.04         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 
        5.10        36.20        20.35        15.78        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       13.84        22.06         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
        0.69         3.95         9.83        12.43        14.93        17.92 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
        4.96        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08         0.23        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        4.77        21.90        15.35        19.82        23.80        15.65 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       41.33         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       11.11         7.40         9.44         8.05        13.28         7.56 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        9.14        12.92        12.46        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       15.45        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       14.14         0.39        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       13.32        11.51        12.76        66.28         0.69 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              8.22               0.13 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             84.10              75.12 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             22.11              13.84 
[1] "8.2 - 84.1 (22.1)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.5"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  16Q LOSS MUTATED         1        0        1         0         8         0
  16Q LOSS WILD-TYPE       0        6       12        26       109         5
                    vv
clus                 STAGE IV
  16Q LOSS MUTATED          0
  16Q LOSS WILD-TYPE        4
D67V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  6
  STAGE IB                 1                 12
  STAGE IIA                0                 26
  STAGE IIB                8                109
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     1   1   8   0
  16Q LOSS WILD-TYPE   7  20 131   4
D67V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                1                  7
  T2                1                 20
  T3                8                131
  T4                0                  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"
D67V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1   8
  16Q LOSS WILD-TYPE  44 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    8
  16Q LOSS WILD-TYPE   44  116
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                1                 44
  1                8                116
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  0
  16Q LOSS WILD-TYPE 77  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    0
  16Q LOSS WILD-TYPE   77    4
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                3                 77
  1                0                  4
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  7
  16Q LOSS WILD-TYPE 75 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    7
  16Q LOSS WILD-TYPE   75   88
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 75
  MALE                  7                 88
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16Q LOSS MUTATED                                     5
  16Q LOSS WILD-TYPE                                 140
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16Q LOSS MUTATED                                       4
  16Q LOSS WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  16Q LOSS MUTATED                                                  0
  16Q LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  16Q LOSS MUTATED                                     1
  16Q LOSS WILD-TYPE                                   0
D67V8, multiclass
                                                  clus
vv                                                 16Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 16Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             140
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D67V9, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 52 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-2J-AABI         TCGA-2J-AABO         TCGA-2J-AABV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-3A-A9I9         TCGA-3A-A9IB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-3A-A9IJ         TCGA-3A-A9IX         TCGA-F2-6880 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F2-A8YN         TCGA-FB-A4P5         TCGA-FB-A5VM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-FB-AAPQ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-FB-AAPY         TCGA-H6-8124 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7887         TCGA-IB-7891 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUT 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-AAUU         TCGA-IB-AAUV         TCGA-LB-A7SX 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-XD-AAUL 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-YY-A8LH 
"16Q LOSS WILD-TYPE" 
D67V10, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED     6   2   0   2
  16Q LOSS WILD-TYPE 102  49   2   2
D67V11, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0                6                102
  R1                2                 49
  R2                0                  2
  RX                2                  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"
D67V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         0    10
  16Q LOSS WILD-TYPE     3                         7   148
D67V13, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   10                148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     0   5
  16Q LOSS WILD-TYPE   3 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    5
  16Q LOSS WILD-TYPE    3  130
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                130
[1] 2 2
[1] FALSE

Clustering(68) Variable = 17P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   27 47
  17P LOSS WILD-TYPE 52 45
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                74                 97 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                47                 45 
$`17P LOSS MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABT 
       23.97        22.26        31.86        15.91        14.47        10.49 
TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IZ 
       20.84         7.36        24.26        28.73        15.06        10.13 
TCGA-3A-A9J0 TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A545 
       12.39        10.98         7.66         3.12        17.00        24.07 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FB-AAQ0 
       12.43        15.95        37.15         7.50        34.82        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
        4.04         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5924 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8005 
       15.78        22.06        21.73        19.50         0.13         3.95 
TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
        9.83        17.92        10.13         6.38        21.60         5.26 
TCGA-IB-7644 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7893 
       12.95        23.80        15.65         4.04        15.81         3.85 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUN 
       17.16        15.85        15.12        21.90        15.88         4.73 
TCGA-IB-AAUO TCGA-IB-AAUU TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        7.86         8.05        12.92        19.20         8.78        15.45 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUI TCGA-XD-AAUL 
       21.24        17.26        16.80         0.39        12.03        13.32 
TCGA-YH-A8SY TCGA-YY-A8LH 
       12.76        66.28 

$`17P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABV TCGA-2L-AAQM TCGA-3A-A9I5 
       22.72        11.84        14.40        21.44        45.47        53.00 
TCGA-3A-A9I7 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR 
       23.61        60.95        84.10        68.52        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6880 
       30.64        31.79        34.09        75.12        71.74         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR 
       19.46         7.10        19.27         5.88        14.76        11.61 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       12.53        23.54         5.10        36.20        20.35        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 
       12.89        13.84         0.92         7.76         0.26        27.62 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 
       20.19        17.03        23.21        12.03         0.69        12.43 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77P TCGA-HZ-A77Q 
       14.93         4.96        21.70        16.14        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
        0.23        49.38         4.77        21.90        15.35        19.82 
TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 
       41.33         3.62        43.79        19.66        21.30        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
        2.47        12.00         7.20        20.88         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        0.26        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
       13.28         7.56         9.14        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RP TCGA-US-A774 
        3.12        15.32         9.40         0.30        23.08        22.85 
TCGA-US-A776 TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-YB-A89D 
       27.75        14.14        18.67        13.81        12.99        11.51 
TCGA-Z5-AAPL 
        0.69 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.13               0.23 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             66.28              84.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            13.895             14.170 
[1] "0.1 - 66.3 (13.9)" "0.2 - 84.1 (14.2)"
[1] "hr=" "1.7"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  17P LOSS MUTATED         0        2        1        12        55         2
  17P LOSS WILD-TYPE       1        4       12        14        62         3
                    vv
clus                 STAGE IV
  17P LOSS MUTATED          2
  17P LOSS WILD-TYPE        2
D68V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 2                  4
  STAGE IB                 1                 12
  STAGE IIA               12                 14
  STAGE IIB               55                 62
  STAGE III                2                  3
  STAGE IV                 2                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    2  6 65  1
  17P LOSS WILD-TYPE  6 15 74  3
D68V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                2                  6
  T2                6                 15
  T3               65                 74
  T4                1                  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"
D68V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   17 57
  17P LOSS WILD-TYPE 28 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     17   57
  17P LOSS WILD-TYPE   28   67
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               17                 28
  1               57                 67
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   31  2
  17P LOSS WILD-TYPE 49  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     31    2
  17P LOSS WILD-TYPE   49    2
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               31                 49
  1                2                  2
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   32 42
  17P LOSS WILD-TYPE 46 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     32   42
  17P LOSS WILD-TYPE   46   53
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               32                 46
  MALE                 42                 53
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17P LOSS MUTATED                                    66
  17P LOSS WILD-TYPE                                  79
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17P LOSS MUTATED                                       7
  17P LOSS WILD-TYPE                                    15
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  17P LOSS MUTATED                                                  0
  17P LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  17P LOSS MUTATED                                     0
  17P LOSS WILD-TYPE                                   1
D68V8, multiclass
                                                  clus
vv                                                 17P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            66
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 17P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              79
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D68V9, continuous
D68V10, continuous
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   39 29  0  2
  17P LOSS WILD-TYPE 69 22  2  2
D68V11, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               39                 69
  R1               29                 22
  R2                0                  2
  RX                2                  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"
D68V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         2    70
  17P LOSS WILD-TYPE     2                         5    88
D68V13, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   70                 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"
D68V14, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1 56
  17P LOSS WILD-TYPE  2 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   56
  17P LOSS WILD-TYPE    2   79
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               56                 79
[1] 2 2
[1] FALSE

Clustering(69) Variable = 17Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   11 10
  17Q LOSS WILD-TYPE 68 82
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                21                150 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                10                 82 
$`17Q LOSS MUTATED`
TCGA-2J-AABK TCGA-2J-AABP TCGA-2L-AAQL TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-AAPP 
       15.91        11.84         9.60        10.98        17.00        15.95 
TCGA-FB-AAQ0 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-HZ-7289 TCGA-HZ-8636 TCGA-HZ-A4BH 
       15.55        24.36         2.01        21.73        17.92         6.38 
TCGA-HZ-A4BK TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-A5SP TCGA-IB-A6UF 
       21.60        23.80         4.04         3.85        15.85        21.90 
TCGA-IB-AAUU TCGA-YH-A8SY TCGA-YY-A8LH 
        8.05        12.76        66.28 

$`17Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABR 
       22.22        22.72        22.26        31.86        14.47        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95        45.47        53.00        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        28.73        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        30.64        15.06        31.79        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       12.39        75.12        71.74         9.70        19.46         7.10 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
        7.66        19.27         3.12         5.88        24.07        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       12.43        11.61        37.15         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5921 
       23.54         4.04         5.03         1.02         8.02         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N 
       36.20        20.35        15.78        17.79        12.89        13.84 
TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       22.06         0.92        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
       16.14        10.13         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       12.95        49.38         4.77        21.90        15.35        19.82 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       15.65        41.33         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ 
       21.30        15.98         2.47        17.16        12.00         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.12        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        9.44        13.28         7.56         9.14        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       10.29        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        27.75        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-Z5-AAPL 
       13.81        12.99        12.03        13.32        11.51         0.69 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              2.01               0.13 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             66.28              84.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             15.85              13.99 
[1] "2.0 - 66.3 (15.8)" "0.1 - 84.1 (14.0)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  17Q LOSS MUTATED         0        0        0         4        15         1
  17Q LOSS WILD-TYPE       1        6       13        22       102         4
                    vv
clus                 STAGE IV
  17Q LOSS MUTATED          1
  17Q LOSS WILD-TYPE        3
D69V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                4                 22
  STAGE IIB               15                102
  STAGE III                1                  4
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED     0   0  21   0
  17Q LOSS WILD-TYPE   8  21 118   4
D69V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                  8
  T2                0                 21
  T3               21                118
  T4                0                  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"
D69V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     5  16
  17Q LOSS WILD-TYPE  40 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5   16
  17Q LOSS WILD-TYPE   40  108
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                5                 40
  1               16                108
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   11  1
  17Q LOSS WILD-TYPE 69  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     11    1
  17Q LOSS WILD-TYPE   69    3
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               11                 69
  1                1                  3
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    6 15
  17Q LOSS WILD-TYPE 72 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      6   15
  17Q LOSS WILD-TYPE   72   80
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                6                 72
  MALE                 15                 80
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17Q LOSS MUTATED                                    16
  17Q LOSS WILD-TYPE                                 129
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17Q LOSS MUTATED                                       3
  17Q LOSS WILD-TYPE                                    19
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  17Q LOSS MUTATED                                                  0
  17Q LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  17Q LOSS MUTATED                                     1
  17Q LOSS WILD-TYPE                                   0
D69V8, multiclass
                                                  clus
vv                                                 17Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            16
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 17Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             129
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D69V9, continuous
D69V10, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED     8   9   0   2
  17Q LOSS WILD-TYPE 100  42   2   2
D69V11, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                8                100
  R1                9                 42
  R2                0                  2
  RX                2                  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"
D69V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       1                         1    19
  17Q LOSS WILD-TYPE     2                         6   139
D69V13, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   19                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  15
  17Q LOSS WILD-TYPE   3 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   15
  17Q LOSS WILD-TYPE    3  120
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               15                120
[1] 2 2
[1] FALSE

Clustering(70) Variable = 18P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   26 24
  18P LOSS WILD-TYPE 53 68
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                50                121 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                24                 68 
$`18P LOSS MUTATED`
TCGA-2J-AABK TCGA-2J-AABR TCGA-2L-AAQI TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IH 
       15.91        14.40         3.39        23.61         7.36        28.73 
TCGA-3A-A9IU TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
       15.06        12.39        71.74         7.66        19.27         3.12 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.76        12.43        11.61        37.15         8.02        15.78 
TCGA-H6-A45N TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-A49G TCGA-HZ-A4BH 
       13.84        17.03        23.21         9.83        21.70         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7647 TCGA-IB-7885 
       21.60        10.85         1.08        12.95        21.90        41.33 
TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        4.04        15.81        19.66         2.47        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-AAUM TCGA-IB-AAUP TCGA-IB-AAUU 
        7.20        15.12        21.90         0.26        14.17         8.05 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-RB-AA9M TCGA-S4-A8RM TCGA-US-A77G TCGA-XD-AAUG 
       19.20         8.78         9.40        21.24         0.39        13.81 
TCGA-XD-AAUI TCGA-YH-A8SY 
       12.03        12.76 

$`18P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        22.26        31.86        14.47        11.84 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       10.49         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IJ 
        9.60        45.47        53.00        20.84        24.26        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV 
       84.10        68.52        63.85        50.70        30.64        31.79 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       34.09        10.13        75.12        10.98         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAPS 
        7.10        17.00         5.88        24.07        15.95         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       17.79        12.89        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8002 
        7.76         0.13         0.26        27.62        20.19        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
        0.69         3.95        12.43        14.93        17.92         4.96 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 
       16.14        10.13         5.26         0.23        49.38         4.77 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7887 TCGA-IB-7888 
       15.35        19.82        23.80        15.65         3.62        43.79 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8127 TCGA-IB-A5ST TCGA-IB-A6UG 
       21.30         3.85        15.98        17.16        20.88         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR 
        8.22        15.88         4.73         7.86         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX 
        7.40         9.44        13.28         7.56         9.14        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29        15.45        13.68         3.12        15.32 
TCGA-RL-AAAS TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
        0.30        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUL TCGA-YB-A89D TCGA-YY-A8LH 
       14.14        18.67        12.99        13.32        11.51        66.28 
TCGA-Z5-AAPL 
        0.69 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.26               0.13 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             71.74              84.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            13.825             14.930 
[1] "0.3 - 71.7 (13.8)" "0.1 - 84.1 (14.9)"
[1] "hr=" "1"  
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  18P LOSS MUTATED         0        2        3         8        33         3
  18P LOSS WILD-TYPE       1        4       10        18        84         2
                    vv
clus                 STAGE IV
  18P LOSS MUTATED          2
  18P LOSS WILD-TYPE        2
D70V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 2                  4
  STAGE IB                 3                 10
  STAGE IIA                8                 18
  STAGE IIB               33                 84
  STAGE III                3                  2
  STAGE IV                 2                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    3  5 41  2
  18P LOSS WILD-TYPE  5 16 98  2
D70V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                3                  5
  T2                5                 16
  T3               41                 98
  T4                2                  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"
D70V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   13 37
  18P LOSS WILD-TYPE 32 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     13   37
  18P LOSS WILD-TYPE   32   87
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               13                 32
  1               37                 87
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   25  2
  18P LOSS WILD-TYPE 55  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     25    2
  18P LOSS WILD-TYPE   55    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               25                 55
  1                2                  2
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   20 31
  18P LOSS WILD-TYPE 58 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     20   31
  18P LOSS WILD-TYPE   58   64
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               20                 58
  MALE                 31                 64
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18P LOSS MUTATED                                    45
  18P LOSS WILD-TYPE                                 100
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18P LOSS MUTATED                                       4
  18P LOSS WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  18P LOSS MUTATED                                                  1
  18P LOSS WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  18P LOSS MUTATED                                     0
  18P LOSS WILD-TYPE                                   1
D70V8, multiclass
                                                  clus
vv                                                 18P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            45
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 18P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D70V9, continuous
D70V10, continuous
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   30 17  0  1
  18P LOSS WILD-TYPE 78 34  2  3
D70V11, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               30                 78
  R1               17                 34
  R2                0                  2
  RX                1                  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"
D70V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       1                         2    46
  18P LOSS WILD-TYPE     2                         5   112
D70V13, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   46                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"
D70V14, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2 40
  18P LOSS WILD-TYPE  1 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   40
  18P LOSS WILD-TYPE    1   95
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               40                 95
[1] 2 2
[1] FALSE

Clustering(71) Variable = 18Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   39 56
  18Q LOSS WILD-TYPE 40 36
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                95                 76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                56                 36 
$`18Q LOSS MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH 
       23.97         9.63        19.96        22.22        22.72        22.26 
TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU 
       31.86        15.91        14.47        14.40        10.49         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9J0 
       23.61        20.84         7.36        28.73        15.06        12.39 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       71.74        10.98         7.66        19.27         3.12        17.00 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPY 
       24.07        14.76        11.61        37.15        12.53        34.82 
TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5923 TCGA-FZ-5924 
       15.55         5.03         1.02         8.02        20.35        15.78 
TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7925 
       17.79        12.89        13.84        22.06        19.50        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I 
       17.03        23.21         9.83        17.92        21.70        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
        6.38        21.60         5.26        10.85         1.08        12.95 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7889 TCGA-IB-7890 
       21.90        15.35        23.80        41.33        15.81        19.66 
TCGA-IB-7893 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
        3.85         2.47        17.16        12.00        15.85         7.20 
TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
       15.12        21.90         1.35         8.22         0.26         4.73 
TCGA-IB-AAUP TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W 
       14.17         8.05         9.14        12.92        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.45         3.12         9.40        21.24        17.26        23.08 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY 
        0.39        13.81        12.03        13.32        12.76 

$`18Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9I5 
        2.17         2.63        20.61        11.84        45.47        53.00 
TCGA-3A-A9IC TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        60.95        84.10        68.52        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6880 
       30.64        31.79        34.09        10.13        75.12         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-FB-A4P5 TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS 
       19.46         7.10         5.88        12.43        15.95         7.50 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
       23.54         4.04        24.36         2.01         5.10        36.20 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
       21.73         0.92         7.76         0.13         0.26        27.62 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
       12.03         0.69         3.95        12.43        14.93         4.96 
TCGA-HZ-A49H TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-7654 
       16.14         0.23        49.38         4.77        19.82        15.65 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-A5ST 
        4.04         3.62        43.79        21.30        15.98        20.88 
TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
       15.88         7.86         6.02        11.11         7.40         9.44 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-RB-A7B8 
       13.28         7.56        12.46        10.29        13.68        15.32 
TCGA-RL-AAAS TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77J 
        0.30        22.85        27.75        16.80        14.14        18.67 
TCGA-XD-AAUH TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.99        11.51        66.28         0.69 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.26               0.13 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             71.74              84.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             14.47              13.48 
[1] "0.3 - 71.7 (14.5)" "0.1 - 84.1 (13.5)"
[1] "hr=" "1.5"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  18Q LOSS MUTATED         0        2        5        19        62         5
  18Q LOSS WILD-TYPE       1        4        8         7        55         0
                    vv
clus                 STAGE IV
  18Q LOSS MUTATED          4
  18Q LOSS WILD-TYPE        0
D71V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 2                  4
  STAGE IB                 5                  8
  STAGE IIA               19                  7
  STAGE IIB               62                 55
  STAGE III                5                  0
  STAGE IV                 4                  0
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    3  9 81  4
  18Q LOSS WILD-TYPE  5 12 58  0
D71V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                3                  5
  T2                9                 12
  T3               81                 58
  T4                4                  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"
D71V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   27 69
  18Q LOSS WILD-TYPE 18 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     27   69
  18Q LOSS WILD-TYPE   18   55
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               27                 18
  1               69                 55
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   48  4
  18Q LOSS WILD-TYPE 32  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     48    4
  18Q LOSS WILD-TYPE   32    0
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               48                 32
  1                4                  0
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   40 57
  18Q LOSS WILD-TYPE 38 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     40   57
  18Q LOSS WILD-TYPE   38   38
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               40                 38
  MALE                 57                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18Q LOSS MUTATED                                    86
  18Q LOSS WILD-TYPE                                  59
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18Q LOSS MUTATED                                       9
  18Q LOSS WILD-TYPE                                    13
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  18Q LOSS MUTATED                                                  1
  18Q LOSS WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  18Q LOSS MUTATED                                     0
  18Q LOSS WILD-TYPE                                   1
D71V8, multiclass
                                                  clus
vv                                                 18Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            86
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 18Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              59
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            13
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D71V9, continuous
D71V10, continuous
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED   54 34  1  3
  18Q LOSS WILD-TYPE 54 17  1  1
D71V11, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               54                 54
  R1               34                 17
  R2                1                  1
  RX                3                  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"
D71V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       3                         3    88
  18Q LOSS WILD-TYPE     0                         4    70
D71V13, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    3                  0
  BLACK OR AFRICAN AMERICAN                3                  4
  WHITE                                   88                 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"
D71V14, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2 68
  18Q LOSS WILD-TYPE  1 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   68
  18Q LOSS WILD-TYPE    1   67
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               68                 67
[1] 2 2
[1] FALSE

Clustering(72) Variable = 19P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    8  9
  19P LOSS WILD-TYPE 71 83
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                154 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 9                 83 
$`19P LOSS MUTATED`
TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABP TCGA-3A-A9IU TCGA-3A-A9J0 TCGA-FB-AAPP 
       31.86        14.47        11.84        15.06        12.39        15.95 
TCGA-H6-8124 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-IB-7646 TCGA-IB-7885 
       12.89         0.13         3.95        17.92         4.77        41.33 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-L1-A7W4 TCGA-LB-A7SX 
       21.90         1.35         8.22         9.14        12.92 

$`19P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABT 
       22.22        22.72        22.26        15.91        14.40        10.49 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        9.60        45.47        53.00        23.61        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        28.73        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY 
       50.70        30.64        31.79        34.09        10.13        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
       19.27         3.12        17.00         5.88        24.07        14.76 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       12.43        11.61        37.15         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       23.54        15.55         4.04         5.03         1.02         8.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 
       24.36         2.01         5.10        36.20        20.35        15.78 
TCGA-FZ-5926 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       17.79        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
        7.76         0.26        27.62        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
       12.03         0.69         9.83        12.43        14.93         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       21.70        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
       10.85         1.08         0.23        12.95        49.38        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7887 
       15.35        19.82        23.80        15.65         4.04         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
       20.88        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
        6.02        11.11         7.40         9.44         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        7.56        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       13.68         3.12        15.32         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.13               0.23 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             41.33              84.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             12.89              14.58 
[1] "0.1 - 41.3 (12.9)" "0.2 - 84.1 (14.6)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  19P LOSS MUTATED         0        0        0         1        15         0
  19P LOSS WILD-TYPE       1        6       13        25       102         5
                    vv
clus                 STAGE IV
  19P LOSS MUTATED          1
  19P LOSS WILD-TYPE        3
D72V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                1                 25
  STAGE IIB               15                102
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED     0   0  17   0
  19P LOSS WILD-TYPE   8  21 122   4
D72V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                0                  8
  T2                0                 21
  T3               17                122
  T4                0                  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"
D72V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2  15
  19P LOSS WILD-TYPE  43 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   15
  19P LOSS WILD-TYPE   43  109
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                2                 43
  1               15                109
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    9  1
  19P LOSS WILD-TYPE 71  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9    1
  19P LOSS WILD-TYPE   71    3
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                9                 71
  1                1                  3
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    8  9
  19P LOSS WILD-TYPE 70 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8    9
  19P LOSS WILD-TYPE   70   86
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                8                 70
  MALE                  9                 86
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19P LOSS MUTATED                                    15
  19P LOSS WILD-TYPE                                 130
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19P LOSS MUTATED                                       1
  19P LOSS WILD-TYPE                                    21
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  19P LOSS MUTATED                                                  0
  19P LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  19P LOSS MUTATED                                     1
  19P LOSS WILD-TYPE                                   0
D72V8, multiclass
                                                  clus
vv                                                 19P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 19P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             130
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D72V9, continuous
D72V10, continuous
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED   10  6  1  0
  19P LOSS WILD-TYPE 98 45  1  4
D72V11, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               10                 98
  R1                6                 45
  R2                1                  1
  RX                0                  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"
D72V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         1    16
  19P LOSS WILD-TYPE     3                         6   142
D72V13, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   16                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  14
  19P LOSS WILD-TYPE   3 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   14
  19P LOSS WILD-TYPE    3  121
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               14                121
[1] 2 2
[1] FALSE

Clustering(73) Variable = 19Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    4  7
  19Q LOSS WILD-TYPE 75 85
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                11                160 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                 85 
$`19Q LOSS MUTATED`
TCGA-2J-AABI TCGA-2J-AABO TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-H6-8124 TCGA-HZ-8005 
       31.86        14.47        15.95        37.15        12.89         3.95 
TCGA-HZ-8636 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-A7LX TCGA-L1-A7W4 
       17.92         4.77        41.33         8.22         9.14 

$`19Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR 
       22.22        22.72        22.26        15.91        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       10.49         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
       12.95         9.60        45.47        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        28.73        60.95        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        30.64        15.06        31.79        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        12.39        75.12        71.74        10.98         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN 
       19.46         7.10         7.66        19.27         3.12        17.00 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPS 
        5.88        24.07        14.76        12.43        11.61         7.50 
TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.53        34.82        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
       20.35        15.78        17.79        13.84        22.06        21.73 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
        0.92        19.50         7.76         0.13         0.26        27.62 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
       20.19        17.03        23.21        12.03         0.69         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
       12.43        14.93         4.96        21.70        16.14        10.13 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
        6.38        21.60         5.26        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       12.95        49.38        21.90        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       15.65         4.04         3.62        43.79        15.81        19.66 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       21.30         3.85        15.98         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.85         7.20        15.12        20.88        21.90         1.35 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       11.11         7.40         9.44         8.05        13.28         7.56 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
       12.92        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       13.68         3.12        15.32         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              3.95               0.13 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             41.33              84.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            14.470             14.155 
[1] "4.0 - 41.3 (14.5)" "0.1 - 84.1 (14.2)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  19Q LOSS MUTATED         0        0        0         1         9         0
  19Q LOSS WILD-TYPE       1        6       13        25       108         5
                    vv
clus                 STAGE IV
  19Q LOSS MUTATED          1
  19Q LOSS WILD-TYPE        3
D73V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                1                 25
  STAGE IIB                9                108
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED     0   0  11   0
  19Q LOSS WILD-TYPE   8  21 128   4
D73V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                0                  8
  T2                0                 21
  T3               11                128
  T4                0                  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"
D73V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2   9
  19Q LOSS WILD-TYPE  43 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    9
  19Q LOSS WILD-TYPE   43  115
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                2                 43
  1                9                115
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    6  1
  19Q LOSS WILD-TYPE 74  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    1
  19Q LOSS WILD-TYPE   74    3
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                6                 74
  1                1                  3
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    5  6
  19Q LOSS WILD-TYPE 73 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5    6
  19Q LOSS WILD-TYPE   73   89
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                5                 73
  MALE                  6                 89
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19Q LOSS MUTATED                                    10
  19Q LOSS WILD-TYPE                                 135
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19Q LOSS MUTATED                                       1
  19Q LOSS WILD-TYPE                                    21
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  19Q LOSS MUTATED                                                  0
  19Q LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  19Q LOSS MUTATED                                     0
  19Q LOSS WILD-TYPE                                   1
D73V8, multiclass
                                                  clus
vv                                                 19Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 19Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             135
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            21
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D73V9, continuous
D73V10, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED     7   3   1   0
  19Q LOSS WILD-TYPE 101  48   1   4
D73V11, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                7                101
  R1                3                 48
  R2                1                  1
  RX                0                  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"
D73V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0    11
  19Q LOSS WILD-TYPE     3                         7   147
D73V13, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   11                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0   9
  19Q LOSS WILD-TYPE   3 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    9
  19Q LOSS WILD-TYPE    3  126
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                9                126
[1] 2 2
[1] FALSE

Clustering(74) Variable = 20P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    8  9
  20P LOSS WILD-TYPE 71 83
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                17                154 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 83 
$`20P LOSS MUTATED`
TCGA-2J-AABH TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9IB TCGA-3A-A9IC TCGA-FB-A78T 
       22.26        22.49        12.95         7.36        24.26        12.43 
TCGA-FB-AAQ1 TCGA-FZ-5920 TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-IB-7887 
        4.04         2.01        21.70        10.13        21.60         3.62 
TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUU TCGA-LB-A7SX TCGA-M8-A5N4 
       21.90        15.88         8.05        12.92        19.20 

$`20P LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        31.86        15.91        14.47        11.84 
TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.40        10.49         9.11        21.44         4.70         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IH 
        9.60        45.47        53.00        23.61        20.84        28.73 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        84.10        68.52        63.85        50.70        30.64 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        31.79        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
       19.27         3.12        17.00         5.88        24.07        14.76 
TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
       11.61        15.95        37.15         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       23.54        15.55         5.03         1.02         8.02        24.36 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 TCGA-H6-8124 
        5.10        36.20        20.35        15.78        17.79        12.89 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       13.84        22.06        21.73         0.92        19.50         7.76 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
        0.13         0.26        27.62        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P 
       17.92         4.96        16.14         6.38         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        12.95        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       15.35        19.82        23.80        15.65        41.33         4.04 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
        2.47        17.16        12.00        15.85         7.20        15.12 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88         1.35         8.22         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         9.44        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE 
        7.56         9.14        12.46        10.29         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       13.68         3.12        15.32         9.40         0.30        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        27.75        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              2.01               0.13 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             24.26              84.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            12.950             14.285 
[1] "2.0 - 24.3 (12.9)" "0.1 - 84.1 (14.3)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  20P LOSS MUTATED         0        0        0         2        15         1
  20P LOSS WILD-TYPE       1        6       13        24       102         4
                    vv
clus                 STAGE IV
  20P LOSS MUTATED          0
  20P LOSS WILD-TYPE        4
D74V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                2                 24
  STAGE IIB               15                102
  STAGE III                1                  4
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED     0   1  16   1
  20P LOSS WILD-TYPE   8  20 123   3
D74V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                0                  8
  T2                1                 20
  T3               16                123
  T4                1                  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"
D74V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3  15
  20P LOSS WILD-TYPE  42 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3   15
  20P LOSS WILD-TYPE   42  109
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                3                 42
  1               15                109
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    8  0
  20P LOSS WILD-TYPE 72  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8    0
  20P LOSS WILD-TYPE   72    4
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                8                 72
  1                0                  4
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    8 10
  20P LOSS WILD-TYPE 70 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   10
  20P LOSS WILD-TYPE   70   85
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                 70
  MALE                 10                 85
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20P LOSS MUTATED                                    16
  20P LOSS WILD-TYPE                                 129
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20P LOSS MUTATED                                       2
  20P LOSS WILD-TYPE                                    20
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  20P LOSS MUTATED                                                  0
  20P LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  20P LOSS MUTATED                                     0
  20P LOSS WILD-TYPE                                   1
D74V8, multiclass
                                                  clus
vv                                                 20P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            16
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 20P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             129
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            20
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D74V9, continuous
D74V10, continuous
                    vv
clus                 R0 R1 R2 RX
  20P LOSS MUTATED    9  9  0  0
  20P LOSS WILD-TYPE 99 42  2  4
D74V11, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                9                 99
  R1                9                 42
  R2                0                  2
  RX                0                  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"
D74V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         2    15
  20P LOSS WILD-TYPE     3                         5   143
D74V13, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   15                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  14
  20P LOSS WILD-TYPE   3 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   14
  20P LOSS WILD-TYPE    3  121
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               14                121
[1] 2 2
[1] FALSE

Clustering(75) Variable = 20Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    0  3
  20Q LOSS WILD-TYPE 79 89
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                168 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 89 
$`20Q LOSS MUTATED`
TCGA-2L-AAQE TCGA-HZ-A49I TCGA-LB-A7SX 
       22.49        10.13        12.92 

$`20Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
       22.22        22.72        22.26        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       11.84        14.40        10.49         9.11        21.44         4.70 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 
        3.39        12.95         9.60        45.47        53.00        23.61 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        30.64        15.06        31.79 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.70        19.46         7.10         7.66        19.27         3.12 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR 
       17.00         5.88        24.07        14.76        12.43        11.61 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       15.95        37.15         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       15.55         4.04         5.03         1.02         8.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5924 TCGA-FZ-5926 
        2.01         5.10        36.20        20.35        15.78        17.79 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       12.89        13.84        22.06        21.73         0.92        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
        7.76         0.13         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03         0.69         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
       14.93        17.92         4.96        21.70        16.14         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
       21.60         5.26        10.85         1.08         0.23        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       49.38         4.77        21.90        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       15.65        41.33         4.04         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       19.66        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       12.00        15.85         7.20        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU 
       14.17         6.02        11.11         7.40         9.44         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
       13.28         7.56         9.14        12.46        10.29        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        8.78        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        0.30        21.24        17.26        23.08        22.85        27.75 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       16.80        14.14         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        13.32        11.51        12.76        66.28         0.69 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             10.13               0.13 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             22.49              84.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            12.920             14.285 
[1] "10.1 - 22.5 (12.9)" "0.1 - 84.1 (14.3)" 
[1] "hr=" "2"  
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  20Q LOSS MUTATED         0        0        0         0         4         0
  20Q LOSS WILD-TYPE       1        6       13        26       113         5
                    vv
clus                 STAGE IV
  20Q LOSS MUTATED          0
  20Q LOSS WILD-TYPE        4
D75V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 0                 13
  STAGE IIA                0                 26
  STAGE IIB                4                113
  STAGE III                0                  5
  STAGE IV                 0                  4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     0   0   4   0
  20Q LOSS WILD-TYPE   8  21 135   4
D75V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                0                  8
  T2                0                 21
  T3                4                135
  T4                0                  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"
D75V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   4
  20Q LOSS WILD-TYPE  45 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    4
  20Q LOSS WILD-TYPE   45  120
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                0                 45
  1                4                120
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  0
  20Q LOSS WILD-TYPE 79  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    0
  20Q LOSS WILD-TYPE   79    4
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                1                 79
  1                0                  4
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  3
  20Q LOSS WILD-TYPE 77 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    3
  20Q LOSS WILD-TYPE   77   92
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 77
  MALE                  3                 92
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20Q LOSS MUTATED                                     4
  20Q LOSS WILD-TYPE                                 141
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                    22
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  20Q LOSS MUTATED                                                  0
  20Q LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  20Q LOSS MUTATED                                     0
  20Q LOSS WILD-TYPE                                   1
D75V8, multiclass
                                                  clus
vv                                                 20Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 20Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             141
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            22
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D75V9, continuous
D75V10, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 43 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2J-AABI         TCGA-2J-AABO         TCGA-3A-A9IB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-3A-A9IJ         TCGA-3A-A9IR         TCGA-3A-A9IX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FB-AAPY         TCGA-H6-8124         TCGA-H8-A6C1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P1         TCGA-IB-7644 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7891         TCGA-IB-8126 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-IB-AAUV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUI         TCGA-XD-AAUL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-YY-A8LH 
"20Q LOSS WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     2   2   0   0
  20Q LOSS WILD-TYPE 106  49   2   4
D75V11, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                2                106
  R1                2                 49
  R2                0                  2
  RX                0                  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"
D75V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         1     3
  20Q LOSS WILD-TYPE     3                         6   155
D75V13, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    3                155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   3
  20Q LOSS WILD-TYPE   3 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    3
  20Q LOSS WILD-TYPE    3  132
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                3                132
[1] 2 2
[1] FALSE

Clustering(76) Variable = 21Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   23 29
  21Q LOSS WILD-TYPE 56 63
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                52                119 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                 63 
$`21Q LOSS MUTATED`
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABT TCGA-2J-AABU TCGA-2L-AAQE 
       15.91        14.47        11.84        10.49         9.11        22.49 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IS TCGA-3A-A9IZ TCGA-3A-A9J0 
        9.60        45.47        20.84        30.64        10.13        12.39 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPY 
        3.12        17.00        24.07        12.43        15.95        34.82 
TCGA-FB-AAQ0 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5924 TCGA-H6-8124 TCGA-H8-A6C1 
       15.55         2.01         5.10        15.78        12.89        22.06 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-A4BH 
        0.92        19.50         0.13         3.95        17.92         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7649 
       21.60         5.26         1.08        12.95         4.77        15.35 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-A5SP TCGA-IB-A5SS 
       19.82        41.33         4.04         3.62        15.85        15.12 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUU 
       21.90         1.35         8.22         7.86        14.17         8.05 
TCGA-OE-A75W TCGA-US-A77G TCGA-YB-A89D TCGA-YY-A8LH 
        8.78         0.39        11.51        66.28 

$`21Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABR TCGA-2J-AABV 
       22.22        22.72        22.26        31.86        14.40        21.44 
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB 
        4.70         3.39        12.95        53.00        23.61         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        28.73        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3E-AAAY TCGA-3E-AAAZ 
       50.70        15.06        31.79        34.09        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.70        19.46         7.10         7.66        19.27 
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
        5.88        14.76        11.61        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 
       23.54         4.04         5.03         1.02         8.02        24.36 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7920 
       36.20        20.35        17.79        13.84        21.73         7.76 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
        0.69         9.83        12.43        14.93         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7647 
       16.14        10.13        10.85         0.23        49.38        21.90 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       23.80        15.65        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ 
        3.85        15.98         2.47        17.16        12.00         7.20 
TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUQ TCGA-IB-AAUR 
       20.88        15.88         0.26         4.73         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX 
        7.40         9.44        13.28         7.56         9.14        12.92 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29        19.20        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        21.24        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUG 
       22.85        27.75        16.80        14.14        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.99        12.03        13.32        12.76         0.69 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.13               0.23 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             66.28              84.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             12.66              14.93 
[1] "0.1 - 66.3 (12.7)" "0.2 - 84.1 (14.9)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  21Q LOSS MUTATED         0        0        1         6        44         0
  21Q LOSS WILD-TYPE       1        6       12        20        73         5
                    vv
clus                 STAGE IV
  21Q LOSS MUTATED          2
  21Q LOSS WILD-TYPE        2
D76V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  6
  STAGE IB                 1                 12
  STAGE IIA                6                 20
  STAGE IIB               44                 73
  STAGE III                0                  5
  STAGE IV                 2                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    0  3 50  0
  21Q LOSS WILD-TYPE  8 18 89  4
D76V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                0                  8
  T2                3                 18
  T3               50                 89
  T4                0                  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"
D76V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    8 45
  21Q LOSS WILD-TYPE 37 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      8   45
  21Q LOSS WILD-TYPE   37   79
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                8                 37
  1               45                 79
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   30  2
  21Q LOSS WILD-TYPE 50  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     30    2
  21Q LOSS WILD-TYPE   50    2
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               30                 50
  1                2                  2
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   20 33
  21Q LOSS WILD-TYPE 58 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     20   33
  21Q LOSS WILD-TYPE   58   62
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               20                 58
  MALE                 33                 62
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  21Q LOSS MUTATED                                    47
  21Q LOSS WILD-TYPE                                  98
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  21Q LOSS MUTATED                                       5
  21Q LOSS WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  21Q LOSS MUTATED                                                  0
  21Q LOSS WILD-TYPE                                                4
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  21Q LOSS MUTATED                                     1
  21Q LOSS WILD-TYPE                                   0
D76V8, multiclass
                                                  clus
vv                                                 21Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            47
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 21Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D76V9, continuous
D76V10, continuous
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   30 20  0  1
  21Q LOSS WILD-TYPE 78 31  2  3
D76V11, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               30                 78
  R1               20                 31
  R2                0                  2
  RX                1                  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"
D76V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       0                         1    50
  21Q LOSS WILD-TYPE     3                         6   108
D76V13, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   50                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    2 38
  21Q LOSS WILD-TYPE  1 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   38
  21Q LOSS WILD-TYPE    1   97
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               38                 97
[1] 2 2
[1] FALSE

Clustering(77) Variable = 22Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   23 20
  22Q LOSS WILD-TYPE 56 72
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                43                128 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                20                 72 
$`22Q LOSS MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABT 
        2.63        22.72        22.26        31.86        14.47        10.49 
TCGA-2L-AAQE TCGA-2L-AAQM TCGA-3A-A9IC TCGA-3A-A9IL TCGA-3A-A9IU TCGA-F2-6879 
       22.49        45.47        24.26        84.10        15.06        10.98 
TCGA-F2-A44H TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       19.27        12.43        11.61        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5924 TCGA-HZ-8636 TCGA-HZ-A4BH 
        5.03        24.36         2.01        15.78        17.92         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7646 TCGA-IB-7886 
       21.60         5.26         1.08         0.23         4.77         4.04 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO 
       17.16        15.85        21.90         8.22        15.88         7.86 
TCGA-IB-AAUU TCGA-OE-A75W TCGA-PZ-A5RE TCGA-RB-AA9M TCGA-XD-AAUL TCGA-YB-A89D 
        8.05         8.78        15.45         9.40        13.32        11.51 
TCGA-YY-A8LH 
       66.28 

$`22Q LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.91        11.84        14.40         9.11        21.44         4.70 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        53.00        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR 
        7.36        28.73        60.95        68.52        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       30.64        31.79        34.09        10.13        12.39        75.12 
TCGA-3E-AAAZ TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A7TX 
       71.74         9.70        19.46         7.10         7.66         3.12 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ 
       17.00         5.88        24.07        14.76        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5921 
        7.50        12.53        34.82         1.02         8.02         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
       36.20        20.35        17.79        12.89        13.84        22.06 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       21.73         0.92        19.50         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       27.62        20.19        17.03        23.21        12.03         0.69 
TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
        3.95         9.83        12.43        14.93         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A77P TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
       16.14        10.13        10.85        12.95        49.38        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 
       15.35        19.82        23.80        15.65        41.33         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
        2.47        12.00         7.20        15.12        20.88         1.35 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73        14.17         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        9.44        13.28         7.56         9.14        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS 
       10.29        19.20        13.68         3.12        15.32         0.30 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       21.24        17.26        23.08        22.85        27.75        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       14.14         0.39        18.67        13.81        12.99        12.03 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76         0.69 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.23               0.13 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             84.10              75.12 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            14.470             14.155 
[1] "0.2 - 84.1 (14.5)" "0.1 - 75.1 (14.2)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  22Q LOSS MUTATED         1        0        1         8        32         0
  22Q LOSS WILD-TYPE       0        6       12        18        85         5
                    vv
clus                 STAGE IV
  22Q LOSS MUTATED          1
  22Q LOSS WILD-TYPE        3
D77V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  6
  STAGE IB                 1                 12
  STAGE IIA                8                 18
  STAGE IIB               32                 85
  STAGE III                0                  5
  STAGE IV                 1                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED     2   3  38   0
  22Q LOSS WILD-TYPE   6  18 101   4
D77V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                2                  6
  T2                3                 18
  T3               38                101
  T4                0                  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"
D77V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    9 32
  22Q LOSS WILD-TYPE 36 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   32
  22Q LOSS WILD-TYPE   36   92
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0                9                 36
  1               32                 92
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   21  1
  22Q LOSS WILD-TYPE 59  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     21    1
  22Q LOSS WILD-TYPE   59    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               21                 59
  1                1                  3
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   13 30
  22Q LOSS WILD-TYPE 65 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     13   30
  22Q LOSS WILD-TYPE   65   65
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               13                 65
  MALE                 30                 65
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  22Q LOSS MUTATED                                    35
  22Q LOSS WILD-TYPE                                 110
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  22Q LOSS MUTATED                                       7
  22Q LOSS WILD-TYPE                                    15
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  22Q LOSS MUTATED                                                  1
  22Q LOSS WILD-TYPE                                                3
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  22Q LOSS MUTATED                                     0
  22Q LOSS WILD-TYPE                                   1
D77V8, multiclass
                                                  clus
vv                                                 22Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            35
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 22Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             110
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               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"
D77V9, continuous
D77V10, continuous
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   27 14  0  0
  22Q LOSS WILD-TYPE 81 37  2  4
D77V11, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               27                 81
  R1               14                 37
  R2                0                  2
  RX                0                  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"
D77V12, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    41
  22Q LOSS WILD-TYPE     2                         6   117
D77V13, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   41                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     0  32
  22Q LOSS WILD-TYPE   3 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0   32
  22Q LOSS WILD-TYPE    3  103
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               32                103
[1] 2 2
[1] FALSE

Clustering(78) Variable = XP LOSS MUTATION ANALYSIS
D78V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED   14 10
  XP LOSS WILD-TYPE 65 82
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               24               147 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               10                82 
$`XP LOSS MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABI TCGA-2J-AABU TCGA-2L-AAQE TCGA-3A-A9I9 TCGA-3A-A9IH 
       23.97        31.86         9.11        22.49        20.84        28.73 
TCGA-3A-A9IL TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAQ0 TCGA-FZ-5924 TCGA-H6-8124 
       84.10        17.00        12.43        15.55        15.78        12.89 
TCGA-HZ-7918 TCGA-HZ-8001 TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-A6UG TCGA-IB-A7LX 
        0.92        23.21         0.23        23.80         1.35         8.22 
TCGA-IB-AAUN TCGA-OE-A75W TCGA-Q3-AA2A TCGA-S4-A8RO TCGA-US-A774 TCGA-YY-A8LH 
        4.73         8.78         3.12        17.26        22.85        66.28 

$`XP LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABR 
       22.72        22.26        15.91        14.47        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       10.49        21.44         4.70         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IJ 
       45.47        53.00        23.61         7.36        24.26        60.95 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        30.64        15.06        31.79 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.70        19.46         7.10         7.66        19.27         3.12 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ 
        5.88        24.07        14.76        11.61        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        34.82        23.54         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        1.02         8.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 
       20.35        17.79        13.84        22.06        21.73        19.50 
TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
        7.76         0.13         0.26        27.62        20.19        17.03 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       12.03         0.69         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       17.92         4.96        21.70        16.14        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 
       21.60         5.26        10.85         1.08        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        15.65        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
        4.04         3.62        43.79        15.81        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.85        15.98         2.47        17.16        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        15.12        20.88        21.90        15.88         0.26 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        7.86        14.17         6.02        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        8.05        13.28         7.56         9.14        12.92        12.46 
TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29        19.20        15.45        13.68        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
        0.30        21.24        23.08        27.75        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       11.51        12.76         0.69 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.23              0.13 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            84.10             75.12 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            16.39             13.84 
[1] "0.2 - 84.1 (16.4)" "0.1 - 75.1 (13.8)"
[1] "hr=" "1.6"
D78V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  XP LOSS MUTATED         1        1        3         5        14         1
  XP LOSS WILD-TYPE       0        5       10        21       103         4
                   vv
clus                STAGE IV
  XP LOSS MUTATED          0
  XP LOSS WILD-TYPE        4
D78V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                1                 5
  STAGE IB                3                10
  STAGE IIA               5                21
  STAGE IIB              14               103
  STAGE III               1                 4
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP LOSS MUTATED     2   3  19   1
  XP LOSS WILD-TYPE   6  18 120   3
D78V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               2                 6
  T2               3                18
  T3              19               120
  T4               1                 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"
D78V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     9  15
  XP LOSS WILD-TYPE  36 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      9   15
  XP LOSS WILD-TYPE   36  109
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0               9                36
  1              15               109
[1] 2 2
[1] FALSE
D78V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   13  0
  XP LOSS WILD-TYPE 67  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     13    0
  XP LOSS WILD-TYPE   67    4
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              13                67
  1               0                 4
[1] 2 2
[1] FALSE
D78V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   12 13
  XP LOSS WILD-TYPE 66 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     12   13
  XP LOSS WILD-TYPE   66   82
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              12                66
  MALE                13                82
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XP LOSS MUTATED                                    22
  XP LOSS WILD-TYPE                                 123
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XP LOSS MUTATED                                       3
  XP LOSS WILD-TYPE                                    19
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  XP LOSS MUTATED                                                  0
  XP LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  XP LOSS MUTATED                                     0
  XP LOSS WILD-TYPE                                   1
D78V8, multiclass
                                                  clus
vv                                                 XP LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 XP LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 4
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D78V9, continuous
D78V10, continuous
                   vv
clus                R0 R1 R2 RX
  XP LOSS MUTATED   19  5  0  1
  XP LOSS WILD-TYPE 89 46  2  3
D78V11, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              19                89
  R1               5                46
  R2               0                 2
  RX               1                 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"
D78V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       1                         0    24
  XP LOSS WILD-TYPE     2                         7   134
D78V13, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  24               134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     1  20
  XP LOSS WILD-TYPE   2 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1   20
  XP LOSS WILD-TYPE    2  115
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              20               115
[1] 2 2
[1] FALSE

Clustering(79) Variable = XQ LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   10  7
  XQ LOSS WILD-TYPE 69 85
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               17               154 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                85 
$`XQ LOSS MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABI TCGA-2J-AABU TCGA-2L-AAQE TCGA-3A-A9I9 TCGA-3A-A9IH 
       23.97        31.86         9.11        22.49        20.84        28.73 
TCGA-3A-A9IL TCGA-F2-A8YN TCGA-FZ-5924 TCGA-H6-8124 TCGA-HZ-7918 TCGA-HZ-A8P1 
       84.10        17.00        15.78        12.89         0.92         0.23 
TCGA-IB-7652 TCGA-IB-A6UG TCGA-IB-AAUN TCGA-OE-A75W TCGA-US-A776 
       23.80         1.35         4.73         8.78        27.75 

$`XQ LOSS WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABR 
       22.72        22.26        15.91        14.47        11.84        14.40 
TCGA-2J-AABT TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       10.49        21.44         4.70         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IJ 
       45.47        53.00        23.61         7.36        24.26        60.95 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        30.64        15.06        31.79 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        12.39        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.70        19.46         7.10         7.66        19.27         3.12 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP 
        5.88        24.07        14.76        12.43        11.61        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       37.15         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-FZ-5919 TCGA-FZ-5920 
        4.04         5.03         1.02         8.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H6-A45N TCGA-H8-A6C1 
        5.10        36.20        20.35        17.79        13.84        22.06 
TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
       21.73        19.50         7.76         0.13         0.26        27.62 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       20.19        17.03        23.21        12.03         0.69         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
        9.83        12.43        14.93        17.92         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        1.08        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       19.82        15.65        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       15.81        19.66        21.30         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       17.16        12.00        15.85         7.20        15.12        20.88 
TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP 
       21.90         8.22        15.88         0.26         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
        6.02        11.11         7.40         9.44         8.05        13.28 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        7.56         9.14        12.92        12.46        10.29        19.20 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       15.45        13.68         3.12        15.32         9.40         0.30 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E 
       21.24        17.26        23.08        22.85        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
        0.39        18.67        13.81        12.99        12.03        13.32 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28         0.69 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.23              0.13 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            84.10             75.12 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            17.00             13.99 
[1] "0.2 - 84.1 (17.0)" "0.1 - 75.1 (14.0)"
[1] "hr=" "1.6"
D79V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  XQ LOSS MUTATED         1        1        2         5         8         0
  XQ LOSS WILD-TYPE       0        5       11        21       109         5
                   vv
clus                STAGE IV
  XQ LOSS MUTATED          0
  XQ LOSS WILD-TYPE        4
D79V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                1                 5
  STAGE IB                2                11
  STAGE IIA               5                21
  STAGE IIB               8               109
  STAGE III               0                 5
  STAGE IV                0                 4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED     2   3  12   0
  XQ LOSS WILD-TYPE   6  18 127   4
D79V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               2                 6
  T2               3                18
  T3              12               127
  T4               0                 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"
D79V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     8   8
  XQ LOSS WILD-TYPE  37 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8    8
  XQ LOSS WILD-TYPE   37  116
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               8                37
  1               8               116
[1] 2 2
[1] FALSE
D79V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   12  0
  XQ LOSS WILD-TYPE 68  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12    0
  XQ LOSS WILD-TYPE   68    4
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              12                68
  1               0                 4
[1] 2 2
[1] FALSE
D79V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    6 11
  XQ LOSS WILD-TYPE 72 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6   11
  XQ LOSS WILD-TYPE   72   84
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               6                72
  MALE                11                84
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XQ LOSS MUTATED                                    13
  XQ LOSS WILD-TYPE                                 132
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XQ LOSS MUTATED                                       3
  XQ LOSS WILD-TYPE                                    19
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  XQ LOSS MUTATED                                                  1
  XQ LOSS WILD-TYPE                                                3
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  XQ LOSS MUTATED                                     0
  XQ LOSS WILD-TYPE                                   1
D79V8, multiclass
                                                  clus
vv                                                 XQ LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 XQ LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            132
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           19
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              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"
D79V9, continuous
D79V10, continuous
                   vv
clus                R0 R1 R2 RX
  XQ LOSS MUTATED   13  4  0  0
  XQ LOSS WILD-TYPE 95 47  2  4
D79V11, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              13                95
  R1               4                47
  R2               0                 2
  RX               0                 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"
D79V12, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         0    16
  XQ LOSS WILD-TYPE     2                         7   142
D79V13, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  16               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  13
  XQ LOSS WILD-TYPE   3 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   13
  XQ LOSS WILD-TYPE    3  122
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              13               122
[1] 2 2
[1] FALSE
