[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/19775410/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/19783029/transformed.cor.cli.txt"

nPatients in clinical file=185, in cluster file=184, common to both=184
[1] "Reduce the number of clustering variables from 82 to 81."
[1]  81 184
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               18               166 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               18               166 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               50               134 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               50               134 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               170 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               170 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               16               168 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               16               168 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10               174 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10               174 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               20               164 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               20               164 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               173 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               173 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               176 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               176 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               28               156 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               28               156 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               164 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               164 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               177 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               177 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               179 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               179 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               52               132 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               52               132 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48               136 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48               136 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               26               158 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               26               158 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               48               136 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               48               136 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8               176 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8               176 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               172 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               172 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                174 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                174 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                171 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                171 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                171 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                171 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                169 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                169 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                30                154 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                30                154 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                22                162 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                22                162 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                29                155 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                29                155 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                26                158 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                26                158 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                170 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                170 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                162 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                162 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                23                161 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                23                161 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                175 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                175 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                167 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                167 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                28                156 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                28                156 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                172 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                172 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                17                167 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                17                167 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                28                156 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                28                156 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                34                150 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                34                150 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                45                139 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                45                139 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                176 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                176 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               176 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               176 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               13               171 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               13               171 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36               148 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36               148 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8               176 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8               176 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               173 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               173 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               179 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               179 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               36               148 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               36               148 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19               165 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19               165 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               25               159 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               25               159 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               25               159 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               25               159 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9               175 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9               175 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               13               171 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               13               171 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               64               120 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               64               120 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               83               101 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               83               101 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               181 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               181 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               180 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               180 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               41               143 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               41               143 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               168 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               168 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               75               109 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               75               109 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               43               141 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               43               141 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                148 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                148 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                30                154 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                30                154 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                17                167 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                17                167 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                168 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                168 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                20                164 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                20                164 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                28                156 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                28                156 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                164 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                164 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                168 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                168 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                30                154 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                30                154 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                173 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                173 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                171 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                171 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                80                104 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                80                104 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                162 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                162 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                55                129 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                55                129 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               106                 78 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               106                 78 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                165 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                165 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                172 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                172 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                164 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                164 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                179 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                179 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                58                126 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                58                126 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                46                138 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                46                138 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               27               157 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               27               157 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18               166 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18               166 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "NUMBER_PACK_YEARS_SMOKED"            
[15] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 184 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=92,	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=110,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 184 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "RESIDUAL_TUMOR"                "NUMBER_OF_LYMPH_NODES"        
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
  7  24 147   4 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  7  24 147   4 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  7  24 147   4 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  7  24 147   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
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=31, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=29, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, 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    7 10
  1P GAIN WILD-TYPE 79 86
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               17               165 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10                86 
$`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        15.22         9.60        58.98         0.03 
TCGA-FZ-5923 TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-A9TJ TCGA-IB-7646 TCGA-IB-7651 
       20.35        17.49        20.19        19.82         4.77        19.82 
TCGA-IB-A6UG TCGA-IB-AAUM TCGA-M8-A5N4 TCGA-RB-A7B8 TCGA-US-A776 
        1.35         0.26        19.20        15.32        39.98 

$`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 
       42.31        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        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        90.12        68.52        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        12.66        16.37 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
       12.89        13.84        22.06         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7289 TCGA-HZ-7918 
       66.94         8.28        32.15        30.25        21.73         0.92 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
       19.50         7.76         0.13         0.26        27.62        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03        19.59         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-7652 TCGA-IB-7654 
       12.95        49.38        21.90        15.35        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-A7LX 
       15.85         7.20        15.12        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         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-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12         9.40         0.30        24.23        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.13 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            58.98             90.12 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            17.49             14.93 
[1] "0.0 - 59.0 (17.5)" "0.1 - 90.1 (14.9)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  1P GAIN MUTATED         0        0        0         3        12         0
  1P GAIN WILD-TYPE       1        5       15        27       109         5
                   vv
clus                STAGE IV
  1P GAIN MUTATED          2
  1P GAIN WILD-TYPE        3
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                0                15
  STAGE IIA               3                27
  STAGE IIB              12               109
  STAGE III               0                 5
  STAGE IV                2                 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     0   2  14   1
  1P GAIN WILD-TYPE   7  22 133   3
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               0                 7
  T2               2                22
  T3              14               133
  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     5  13
  1P GAIN WILD-TYPE  45 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5   13
  1P GAIN WILD-TYPE   45  116
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               5                45
  1              13               116
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    9  2
  1P GAIN WILD-TYPE 76  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      9    2
  1P GAIN WILD-TYPE   76    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               9                76
  1               2                 3
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    7 11
  1P GAIN WILD-TYPE 76 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      7   11
  1P GAIN WILD-TYPE   76   90
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               7                76
  MALE                11                90
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    13   3
  1P GAIN WILD-TYPE 109  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     13    3
  1P GAIN WILD-TYPE  109   39
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               13               109
  YES               3                39
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1P GAIN MUTATED                                    14
  1P GAIN WILD-TYPE                                 139
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1P GAIN MUTATED                                       2
  1P GAIN WILD-TYPE                                    23
                   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
D1V9, multiclass
                                                  clus
vv                                                 1P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           14
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 1P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            139
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           23
  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"
D1V10, continuous
D1V11, continuous
                   vv
clus                R0 R1 R2 RX
  1P GAIN MUTATED   12  4  1  1
  1P GAIN WILD-TYPE 99 49  4  3
D1V12, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              12                99
  R1               4                49
  R2               1                 4
  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"
D1V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         0    16
  1P GAIN WILD-TYPE    10                         7   145
D1V14, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  16               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"
D1V15, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  11
  1P GAIN WILD-TYPE   4 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   11
  1P GAIN WILD-TYPE    4  125
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              11               125
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   21 27
  1Q GAIN WILD-TYPE 65 69
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               48               134 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               27                69 
$`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        42.31        15.22        12.95 
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9IC TCGA-3A-A9IU TCGA-3E-AAAZ TCGA-F2-A44H 
        9.60        58.98        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 
        0.03        15.95        12.53        15.55         8.02         2.01 
TCGA-FZ-5923 TCGA-FZ-5924 TCGA-H8-A6C1 TCGA-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A7OP 
       20.35        15.78        22.06         4.21         9.50        32.15 
TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A8P1 
       17.49        20.19        17.92         6.38         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-7893 
       19.82         4.77        19.82         4.04        21.30         3.85 
TCGA-IB-8127 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-LB-A8F3 
       17.16        21.90         1.35         8.22         0.26        12.46 
TCGA-M8-A5N4 TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 TCGA-YY-A8LH 
       19.20        15.32        24.23        23.08        39.98        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        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        33.57        60.95        90.12        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       75.12        10.98         9.50        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        12.66        16.37        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-HV-A5A4 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HZ-7289 
       13.84         7.63        66.94         8.28        30.25        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        19.59         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-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
       21.60        10.85         1.08        12.95        49.38        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-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       15.81        19.66        15.98         2.47        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO 
        7.20        15.12        20.88        15.88         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-OE-A75W 
       13.28         7.56         9.14        12.92        10.29         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RO 
       15.45        13.68         3.12         9.40         0.30        17.26 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.13 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            71.74             90.12 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           15.665            14.435 
[1] "0.0 - 71.7 (15.7)" "0.1 - 90.1 (14.4)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  1Q GAIN MUTATED         0        1        1        13        30         1
  1Q GAIN WILD-TYPE       1        4       14        17        91         4
                   vv
clus                STAGE IV
  1Q GAIN MUTATED          3
  1Q GAIN WILD-TYPE        2
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 4
  STAGE IB                1                14
  STAGE IIA              13                17
  STAGE IIB              30                91
  STAGE III               1                 4
  STAGE IV                3                 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     1   4  42   2
  1Q GAIN WILD-TYPE   6  20 105   2
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               1                 6
  T2               4                20
  T3              42               105
  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   17 32
  1Q GAIN WILD-TYPE 33 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17   32
  1Q GAIN WILD-TYPE   33   97
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              17                33
  1              32                97
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   21  3
  1Q GAIN WILD-TYPE 64  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     21    3
  1Q GAIN WILD-TYPE   64    2
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              21                64
  1               3                 2
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   17 33
  1Q GAIN WILD-TYPE 66 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17   33
  1Q GAIN WILD-TYPE   66   68
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              17                66
  MALE                33                68
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   32 10
  1Q GAIN WILD-TYPE 90 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     32   10
  1Q GAIN WILD-TYPE   90   32
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               32                90
  YES              10                32
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1Q GAIN MUTATED                                    43
  1Q GAIN WILD-TYPE                                 110
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1Q GAIN MUTATED                                       5
  1Q GAIN WILD-TYPE                                    20
                   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
D2V9, multiclass
                                                  clus
vv                                                 1Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           43
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 1Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            110
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           20
  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"
D2V10, continuous
D2V11, continuous
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   33 12  1  1
  1Q GAIN WILD-TYPE 78 41  4  3
D2V12, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              33                78
  R1              12                41
  R2               1                 4
  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"
D2V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       5                         2    42
  1Q GAIN WILD-TYPE     6                         5   119
D2V14, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   5                 6
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  42               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"
D2V15, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2  34
  1Q GAIN WILD-TYPE   3 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   34
  1Q GAIN WILD-TYPE    3  102
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              34               102
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   10  4
  2P GAIN WILD-TYPE 76 92
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               168 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                92 
$`2P GAIN MUTATED`
TCGA-2J-AABO TCGA-2L-AAQL TCGA-3A-A9J0 TCGA-FB-A545 TCGA-FB-AAPZ TCGA-HZ-A9TJ 
       14.47         9.60        24.43        12.66        23.54        19.82 
TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-AAUU 
       19.82         4.04         3.85        17.16        15.85         8.05 
TCGA-YB-A89D TCGA-YH-A8SY 
       11.51        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        42.31        31.86        15.91        15.22 
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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        33.57        60.95        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        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         9.50        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 
       16.37         0.03        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-HV-A5A3 
       15.78        17.79        12.89        13.84        22.06         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
        7.63         9.50        66.94         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       17.49        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 
       19.59         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-7652 TCGA-IB-7654 TCGA-IB-7885 
        4.77        21.90        15.35        23.80        15.65        41.33 
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-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-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-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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        16.37        31.27        23.67        66.28        15.35 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             3.85              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            24.43             90.12 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           13.615            15.270 
[1] "3.9 - 24.4 (13.6)" "0.0 - 90.1 (15.3)"
[1] "hr=" "1.6"
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        5       15        28       111         4
                   vv
clus                STAGE IV
  2P GAIN MUTATED          1
  2P GAIN WILD-TYPE        4
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                0                15
  STAGE IIA               2                28
  STAGE IIB              10               111
  STAGE III               1                 4
  STAGE IV                1                 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  13   0
  2P GAIN WILD-TYPE   7  23 134   4
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               0                 7
  T2               1                23
  T3              13               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"
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     3  11
  2P GAIN WILD-TYPE  47 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   11
  2P GAIN WILD-TYPE   47  118
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               3                47
  1              11               118
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    8  1
  2P GAIN WILD-TYPE 77  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8    1
  2P GAIN WILD-TYPE   77    4
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               8                77
  1               1                 4
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3 11
  2P GAIN WILD-TYPE 80 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   11
  2P GAIN WILD-TYPE   80   90
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                80
  MALE                11                90
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    10   4
  2P GAIN WILD-TYPE 112  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     10    4
  2P GAIN WILD-TYPE  112   38
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               10               112
  YES               4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2P GAIN MUTATED                                    12
  2P GAIN WILD-TYPE                                 141
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2P GAIN MUTATED                                       1
  2P GAIN WILD-TYPE                                    24
                   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
D3V9, multiclass
                                                  clus
vv                                                 2P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 2P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            141
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           24
  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"
D3V10, continuous
D3V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED     8   3   0   1
  2P GAIN WILD-TYPE 103  50   5   3
D3V12, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               8               103
  R1               3                50
  R2               0                 5
  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"
D3V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0    14
  2P GAIN WILD-TYPE    11                         7   147
D3V14, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  14               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"
D3V15, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  11
  2P GAIN WILD-TYPE   5 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   11
  2P GAIN WILD-TYPE    5  125
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              11               125
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   12  4
  2Q GAIN WILD-TYPE 74 92
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               16               166 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                4                92 
$`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        24.43        12.66        23.54 
TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-8127 
       10.85        19.82        19.82         4.04         3.85        17.16 
TCGA-IB-A5SP TCGA-IB-AAUU TCGA-YB-A89D TCGA-YH-A8SY 
       15.85         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        42.31        31.86        15.91        15.22        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        58.98        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        33.57        60.95        90.12        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        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         9.50        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        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
        9.50        66.94         8.28        32.15        30.25        17.49 
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        19.59 
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-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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        66.28        15.35 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             3.85              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            24.43             90.12 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           13.615            15.270 
[1] "3.9 - 24.4 (13.6)" "0.0 - 90.1 (15.3)"
[1] "hr=" "1.9"
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        5       15        27       110         4
                   vv
clus                STAGE IV
  2Q GAIN MUTATED          1
  2Q GAIN WILD-TYPE        4
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                0                15
  STAGE IIA               3                27
  STAGE IIB              11               110
  STAGE III               1                 4
  STAGE IV                1                 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  15   0
  2Q GAIN WILD-TYPE   7  23 132   4
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               0                 7
  T2               1                23
  T3              15               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"
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4  12
  2Q GAIN WILD-TYPE  46 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   12
  2Q GAIN WILD-TYPE   46  117
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               4                46
  1              12               117
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    9  1
  2Q GAIN WILD-TYPE 76  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9    1
  2Q GAIN WILD-TYPE   76    4
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               9                76
  1               1                 4
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3 13
  2Q GAIN WILD-TYPE 80 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   13
  2Q GAIN WILD-TYPE   80   88
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               3                80
  MALE                13                88
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    11   5
  2Q GAIN WILD-TYPE 111  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     11    5
  2Q GAIN WILD-TYPE  111   37
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               11               111
  YES               5                37
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2Q GAIN MUTATED                                    13
  2Q GAIN WILD-TYPE                                 140
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2Q GAIN MUTATED                                       2
  2Q GAIN WILD-TYPE                                    23
                   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
D4V9, multiclass
                                                  clus
vv                                                 2Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 2Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            140
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           23
  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"
D4V10, continuous
D4V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    10   3   0   1
  2Q GAIN WILD-TYPE 101  50   5   3
D4V12, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              10               101
  R1               3                50
  R2               0                 5
  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"
D4V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0    16
  2Q GAIN WILD-TYPE    11                         7   145
D4V14, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  16               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"
D4V15, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  12
  2Q GAIN WILD-TYPE   5 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   12
  2Q GAIN WILD-TYPE    5  124
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              12               124
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    4  6
  3P GAIN WILD-TYPE 82 90
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10               172 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                90 
$`3P GAIN MUTATED`
TCGA-2J-AAB6 TCGA-3A-A9J0 TCGA-FB-A5VM TCGA-FB-AAPZ TCGA-HZ-7922 TCGA-HZ-A9TJ 
        9.63        24.43        16.37        23.54         0.13        19.82 
TCGA-IB-7646 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-A6UG 
        4.77        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        42.31        31.86        15.91        14.47        15.22 
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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        32.81        15.06        36.26 
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         9.50 
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        12.66         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP 
        4.21         7.63         9.50        66.94         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       30.25        17.49        21.73         0.92        19.50         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-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       19.59         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-7891 TCGA-IB-7897 
        4.04         3.62        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-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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        39.98        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.13              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            24.43             90.12 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            13.00             15.17 
[1] "0.1 - 24.4 (13.0)" "0.0 - 90.1 (15.2)"
[1] "hr=" "1.4"
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        5       13        28       116         5
                   vv
clus                STAGE IV
  3P GAIN MUTATED          1
  3P GAIN WILD-TYPE        4
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                2                13
  STAGE IIA               2                28
  STAGE IIB               5               116
  STAGE III               0                 5
  STAGE IV                1                 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   7   0
  3P GAIN WILD-TYPE   7  21 140   4
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               0                 7
  T2               3                21
  T3               7               140
  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     5   5
  3P GAIN WILD-TYPE  45 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5    5
  3P GAIN WILD-TYPE   45  124
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               5                45
  1               5               124
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    6  1
  3P GAIN WILD-TYPE 79  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    1
  3P GAIN WILD-TYPE   79    4
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               6                79
  1               1                 4
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  9
  3P GAIN WILD-TYPE 82 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    9
  3P GAIN WILD-TYPE   82   92
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                82
  MALE                 9                92
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     9   0
  3P GAIN WILD-TYPE 113  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9    0
  3P GAIN WILD-TYPE  113   42
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                9               113
  YES               0                42
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3P GAIN MUTATED                                     9
  3P GAIN WILD-TYPE                                 144
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3P GAIN MUTATED                                       1
  3P GAIN WILD-TYPE                                    24
                   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
D5V9, multiclass
                                                  clus
vv                                                 3P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 3P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            144
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           24
  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"
D5V10, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                54 
       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-HV-AA8V        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-7887        TCGA-IB-7891        TCGA-IB-8126 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A7M4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V11, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                44 
       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-XN-A8T5        TCGA-YY-A8LH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED     8   2   0   0
  3P GAIN WILD-TYPE 103  51   5   4
D5V12, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               8               103
  R1               2                51
  R2               0                 5
  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"
D5V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0     9
  3P GAIN WILD-TYPE    11                         7   152
D5V14, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   9               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"
D5V15, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0   8
  3P GAIN WILD-TYPE   5 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    8
  3P GAIN WILD-TYPE    5  128
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               8               128
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    4 16
  3Q GAIN WILD-TYPE 82 80
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               20               162 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16                80 
$`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        24.43        16.37        23.54 
TCGA-FB-AAQ1 TCGA-HV-A5A3 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-A9TJ 
        4.04         4.21         0.13         3.95        17.92        19.82 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-A6UG TCGA-IB-A7LX 
        4.77        21.90        19.66         3.85         1.35         8.22 
TCGA-IB-AAUO TCGA-RB-A7B8 
        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        42.31        31.86        15.91        14.47        15.22 
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        58.98        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        33.57        60.95        90.12        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        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         9.50        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        12.66 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
        0.03        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-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84        22.06         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 
        8.28        32.15        30.25        17.49        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-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03        19.59         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-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-7897 TCGA-IB-8126 
        3.62        43.79        15.81        21.30        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-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ 
       21.90        15.88         0.26         4.73        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-AA9M TCGA-RL-AAAS TCGA-S4-A8RM 
       15.45        13.68         3.12         9.40         0.30        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.13              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            24.43             90.12 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             8.91             15.35 
[1] "0.1 - 24.4 (8.9)"  "0.0 - 90.1 (15.3)"
[1] "hr=" "2.6"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  3Q GAIN MUTATED         0        0        2         3        13         0
  3Q GAIN WILD-TYPE       1        5       13        27       108         5
                   vv
clus                STAGE IV
  3Q GAIN MUTATED          2
  3Q GAIN WILD-TYPE        3
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                2                13
  STAGE IIA               3                27
  STAGE IIB              13               108
  STAGE III               0                 5
  STAGE IV                2                 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  17   0
  3Q GAIN WILD-TYPE   7  21 130   4
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               0                 7
  T2               3                21
  T3              17               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"
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     6  13
  3Q GAIN WILD-TYPE  44 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6   13
  3Q GAIN WILD-TYPE   44  116
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               6                44
  1              13               116
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    8  2
  3Q GAIN WILD-TYPE 77  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8    2
  3Q GAIN WILD-TYPE   77    3
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               8                77
  1               2                 3
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    5 15
  3Q GAIN WILD-TYPE 78 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5   15
  3Q GAIN WILD-TYPE   78   86
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               5                78
  MALE                15                86
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    18   0
  3Q GAIN WILD-TYPE 104  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     18    0
  3Q GAIN WILD-TYPE  104   42
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               18               104
  YES               0                42
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3Q GAIN MUTATED                                    18
  3Q GAIN WILD-TYPE                                 135
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3Q GAIN MUTATED                                       2
  3Q GAIN WILD-TYPE                                    23
                   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
D6V9, multiclass
                                                  clus
vv                                                 3Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 3Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            135
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           23
  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"
D6V10, continuous
D6V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    11   7   0   1
  3Q GAIN WILD-TYPE 100  46   5   3
D6V12, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              11               100
  R1               7                46
  R2               0                 5
  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"
D6V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       1                         0    18
  3Q GAIN WILD-TYPE    10                         7   143
D6V14, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  18               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"
D6V15, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0  16
  3Q GAIN WILD-TYPE   5 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   16
  3Q GAIN WILD-TYPE    5  120
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              16               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 79 93
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               172 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                93 
$`4P GAIN MUTATED`
TCGA-2J-AAB6 TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IS TCGA-3A-A9IV 
        9.63        15.22        45.47        68.52        32.81        36.26 
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        42.31        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        58.98        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        33.57        60.95        90.12        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        24.43        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.50        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        12.66        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
       12.89        13.84        22.06         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 
       66.94         8.28        32.15        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        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-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-A8RO 
        3.12        15.32         9.40         0.30        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
       18.67        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        12.76        66.28        15.35 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.13              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            68.52             90.12 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           16.935            14.995 
[1] "0.1 - 68.5 (16.9)" "0.0 - 90.1 (15.0)"
[1] "hr=" "2.4"
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        5       12        29       115         5
                   vv
clus                STAGE IV
  4P GAIN MUTATED          1
  4P GAIN WILD-TYPE        4
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                3                12
  STAGE IIA               1                29
  STAGE IIB               6               115
  STAGE III               0                 5
  STAGE IV                1                 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 GAIN MUTATED     0   3   8   0
  4P GAIN WILD-TYPE   7  21 139   4
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                 7
  T2               3                21
  T3               8               139
  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  46 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    6
  4P GAIN WILD-TYPE   46  123
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               4                46
  1               6               123
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 83  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   83    4
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               2                83
  1               1                 4
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    6  5
  4P GAIN WILD-TYPE 77 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    5
  4P GAIN WILD-TYPE   77   96
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6                77
  MALE                 5                96
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     5   3
  4P GAIN WILD-TYPE 117  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    3
  4P GAIN WILD-TYPE  117   39
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                5               117
  YES               3                39
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4P GAIN MUTATED                                     6
  4P GAIN WILD-TYPE                                 147
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4P GAIN MUTATED                                       4
  4P GAIN WILD-TYPE                                    21
                   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
D7V9, 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                            147
  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"
D7V10, continuous
D7V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     8   3   0   0
  4P GAIN WILD-TYPE 103  50   5   4
D7V12, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               8               103
  R1               3                50
  R2               0                 5
  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"
D7V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         0    11
  4P GAIN WILD-TYPE    11                         7   150
D7V14, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  11               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"
D7V15, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   7
  4P GAIN WILD-TYPE   4 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    7
  4P GAIN WILD-TYPE    4  129
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               7               129
[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 80 94
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               174 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                94 
$`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        32.81        36.26        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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
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        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.50        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37         0.03        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-HV-A5A3 
       15.78        17.79        12.89        13.84        22.06         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
        7.63         9.50        66.94         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       17.49        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        19.59 
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-A77O TCGA-HZ-A77P 
       16.14        10.13         6.38        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        1.08         0.23        19.82        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-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 
       24.23        17.26        23.08        22.85        39.98        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       16.37        31.27        23.67        12.76        66.28        15.35 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.13              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            68.52             90.12 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           25.365            14.995 
[1] "0.1 - 68.5 (25.4)" "0.0 - 90.1 (15.0)"
[1] "hr=" "3.3"
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        5       12        30       117         5
                   vv
clus                STAGE IV
  4Q GAIN MUTATED          1
  4Q GAIN WILD-TYPE        4
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                3                12
  STAGE IIA               0                30
  STAGE IIB               4               117
  STAGE III               0                 5
  STAGE IV                1                 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 GAIN MUTATED     0   3   5   0
  4Q GAIN WILD-TYPE   7  21 142   4
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                 7
  T2               3                21
  T3               5               142
  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  47 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    4
  4Q GAIN WILD-TYPE   47  125
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               3                47
  1               4               125
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  1
  4Q GAIN WILD-TYPE 85  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    1
  4Q GAIN WILD-TYPE   85    4
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               0                85
  1               1                 4
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    4  4
  4Q GAIN WILD-TYPE 79 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    4
  4Q GAIN WILD-TYPE   79   97
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4                79
  MALE                 4                97
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3   3
  4Q GAIN WILD-TYPE 119  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    3
  4Q GAIN WILD-TYPE  119   39
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                3               119
  YES               3                39
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4Q GAIN MUTATED                                     4
  4Q GAIN WILD-TYPE                                 149
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4Q GAIN MUTATED                                       4
  4Q GAIN WILD-TYPE                                    21
                   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
D8V9, 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                            149
  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"
D8V10, continuous
D8V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     5   3   0   0
  4Q GAIN WILD-TYPE 106  50   5   4
D8V12, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               106
  R1               3                50
  R2               0                 5
  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"
D8V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         0     8
  4Q GAIN WILD-TYPE    11                         7   153
D8V14, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   8               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"
D8V15, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   7
  4Q GAIN WILD-TYPE   5 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    7
  4Q GAIN WILD-TYPE    5  129
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               7               129
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   12 15
  5P GAIN WILD-TYPE 74 81
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               27               155 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               15                81 
$`5P GAIN MUTATED`
TCGA-2J-AABF TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IN 
       22.72        15.22         9.11        45.47        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-AAPP 
       63.85        32.81        36.26         3.12        16.37        15.95 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-HV-A5A6 TCGA-HZ-7289 TCGA-HZ-7922 
       23.54        15.55         4.04        66.94        21.73         0.13 
TCGA-HZ-A77O TCGA-IB-7886 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7LX TCGA-LB-A7SX 
        5.26         4.04        15.85         1.35         8.22        12.92 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-YH-A8SY 
       19.20         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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       33.57        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 
       24.43        75.12        71.74        10.98         9.50        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        12.66 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-A7OP 
       22.06         4.21         7.63         9.50         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       30.25        17.49         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        19.59 
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-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        1.08         0.23        19.82        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-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98         2.47        17.16        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-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-PZ-A5RE 
       13.28         7.56         9.14        12.46        10.29        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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        66.28        15.35 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.13              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            90.12             75.12 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            15.85             14.93 
[1] "0.1 - 90.1 (15.8)" "0.0 - 75.1 (14.9)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  5P GAIN MUTATED         1        0        4         4        17         1
  5P GAIN WILD-TYPE       0        5       11        26       104         4
                   vv
clus                STAGE IV
  5P GAIN MUTATED          0
  5P GAIN WILD-TYPE        5
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 5
  STAGE IB                4                11
  STAGE IIA               4                26
  STAGE IIB              17               104
  STAGE III               1                 4
  STAGE IV                0                 5
[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  20   0
  5P GAIN WILD-TYPE   6  18 127   4
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                 6
  T2               6                18
  T3              20               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"
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     7  18
  5P GAIN WILD-TYPE  43 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   18
  5P GAIN WILD-TYPE   43  111
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               7                43
  1              18               111
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   11  0
  5P GAIN WILD-TYPE 74  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11    0
  5P GAIN WILD-TYPE   74    5
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              11                74
  1               0                 5
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   11 17
  5P GAIN WILD-TYPE 72 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11   17
  5P GAIN WILD-TYPE   72   84
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              11                72
  MALE                17                84
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    20   6
  5P GAIN WILD-TYPE 102  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     20    6
  5P GAIN WILD-TYPE  102   36
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               20               102
  YES               6                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5P GAIN MUTATED                                    19
  5P GAIN WILD-TYPE                                 134
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5P GAIN MUTATED                                       7
  5P GAIN WILD-TYPE                                    18
                   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
D9V9, multiclass
                                                  clus
vv                                                 5P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           19
  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                            134
  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"
D9V10, continuous
D9V11, continuous
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   16 10  0  1
  5P GAIN WILD-TYPE 95 43  5  3
D9V12, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              16                95
  R1              10                43
  R2               0                 5
  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"
D9V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       1                         1    25
  5P GAIN WILD-TYPE    10                         6   136
D9V14, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  25               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"
D9V15, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  19
  5P GAIN WILD-TYPE   4 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   19
  5P GAIN WILD-TYPE    4  117
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              19               117
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   10  9
  5Q GAIN WILD-TYPE 76 87
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               163 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9                87 
$`5Q GAIN MUTATED`
TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IV 
       45.47        90.12        68.52        63.85        32.81        36.26 
TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
        3.12        16.37        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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        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        24.43        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.50        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        12.66         0.03        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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
        9.50        66.94         8.28        32.15        30.25        17.49 
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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-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-OE-A75W 
       13.28         7.56         9.14        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-A779 
       24.23        17.26        23.08        22.85        39.98        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.13              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            90.12             75.12 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            15.95             14.93 
[1] "0.1 - 90.1 (15.9)" "0.0 - 75.1 (14.9)"
[1] "hr=" "1.4"
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        5       11        27       110         5
                   vv
clus                STAGE IV
  5Q GAIN MUTATED          0
  5Q GAIN WILD-TYPE        5
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 5
  STAGE IB                4                11
  STAGE IIA               3                27
  STAGE IIB              11               110
  STAGE III               0                 5
  STAGE IV                0                 5
[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   6  18 135   4
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               1                 6
  T2               6                18
  T3              12               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"
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     6  11
  5Q GAIN WILD-TYPE  44 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      6   11
  5Q GAIN WILD-TYPE   44  118
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               6                44
  1              11               118
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    5  0
  5Q GAIN WILD-TYPE 80  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    0
  5Q GAIN WILD-TYPE   80    5
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               5                80
  1               0                 5
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    8 12
  5Q GAIN WILD-TYPE 75 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8   12
  5Q GAIN WILD-TYPE   75   89
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               8                75
  MALE                12                89
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    15   3
  5Q GAIN WILD-TYPE 107  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     15    3
  5Q GAIN WILD-TYPE  107   39
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               15               107
  YES               3                39
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5Q GAIN MUTATED                                    14
  5Q GAIN WILD-TYPE                                 139
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5Q GAIN MUTATED                                       6
  5Q GAIN WILD-TYPE                                    19
                   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
D10V9, 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                            139
  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"
D10V10, continuous
D10V11, continuous
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED   12  8  0  0
  5Q GAIN WILD-TYPE 99 45  5  4
D10V12, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              12                99
  R1               8                45
  R2               0                 5
  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"
D10V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         1    18
  5Q GAIN WILD-TYPE    11                         6   143
D10V14, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  18               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"
D10V15, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  15
  5Q GAIN WILD-TYPE   4 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   15
  5Q GAIN WILD-TYPE    4  121
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              15               121
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    5  2
  6P GAIN WILD-TYPE 81 94
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               175 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                94 
$`6P GAIN MUTATED`
TCGA-2J-AABF TCGA-3A-A9IO TCGA-FB-AAPZ TCGA-HZ-8005 TCGA-HZ-A9TJ TCGA-LB-A8F3 
       22.72        63.85        23.54         3.95        19.82        12.46 
TCGA-US-A776 
       39.98 

$`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        42.31        31.86        15.91        14.47        15.22 
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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       32.15        30.25        17.49        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-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03        19.59         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-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-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-A779 
        0.30        24.23        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             3.95              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            63.85             90.12 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            22.72             15.06 
[1] "4.0 - 63.9 (22.7)" "0.0 - 90.1 (15.1)"
[1] "hr=" "2.8"
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        5       15        28       118         5
                   vv
clus                STAGE IV
  6P GAIN MUTATED          1
  6P GAIN WILD-TYPE        4
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                0                15
  STAGE IIA               2                28
  STAGE IIB               3               118
  STAGE III               0                 5
  STAGE IV                1                 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   5   0
  6P GAIN WILD-TYPE   7  23 142   4
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               0                 7
  T2               1                23
  T3               5               142
  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     3   3
  6P GAIN WILD-TYPE  47 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    3
  6P GAIN WILD-TYPE   47  126
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               3                47
  1               3               126
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    1  1
  6P GAIN WILD-TYPE 84  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    1
  6P GAIN WILD-TYPE   84    4
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               1                84
  1               1                 4
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    1  6
  6P GAIN WILD-TYPE 82 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    6
  6P GAIN WILD-TYPE   82   95
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               1                82
  MALE                 6                95
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5   2
  6P GAIN WILD-TYPE 117  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    2
  6P GAIN WILD-TYPE  117   40
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                5               117
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6P GAIN MUTATED                                     4
  6P GAIN WILD-TYPE                                 149
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6P GAIN MUTATED                                       2
  6P GAIN WILD-TYPE                                    23
                   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
D11V9, multiclass
                                                  clus
vv                                                 6P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 6P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            149
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           23
  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"
D11V10, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                55 
       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-HV-AA8V        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-7887        TCGA-IB-7891        TCGA-IB-8126 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V11, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                45 
       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-XN-A8T5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-YY-A8LH 
"6P GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED     5   2   0   0
  6P GAIN WILD-TYPE 106  51   5   4
D11V12, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               5               106
  R1               2                51
  R2               0                 5
  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"
D11V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                         1     6
  6P GAIN WILD-TYPE    11                         6   155
D11V14, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   6               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"
D11V15, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0   6
  6P GAIN WILD-TYPE   5 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    6
  6P GAIN WILD-TYPE    5  130
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6               130
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    3  2
  6Q GAIN WILD-TYPE 83 94
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               177 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                94 
$`6Q GAIN MUTATED`
TCGA-2J-AABF TCGA-3A-A9IO TCGA-HZ-8005 TCGA-HZ-A9TJ TCGA-LB-A8F3 
       22.72        63.85         3.95        19.82        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        42.31        31.86        15.91        14.47        15.22 
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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       13.84        22.06         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 
        8.28        32.15        30.25        17.49        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        19.59         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-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-A9Q5 
        8.05        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-S4-A8RP TCGA-US-A774 
        9.40         0.30        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       39.98        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             3.95              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            63.85             90.12 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            19.82             15.12 
[1] "4.0 - 63.9 (19.8)" "0.0 - 90.1 (15.1)"
[1] "hr=" "1.7"
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        5       15        29       119         5
                   vv
clus                STAGE IV
  6Q GAIN MUTATED          1
  6Q GAIN WILD-TYPE        4
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                0                15
  STAGE IIA               1                29
  STAGE IIB               2               119
  STAGE III               0                 5
  STAGE IV                1                 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   4   0
  6Q GAIN WILD-TYPE   7  24 143   4
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               0                 7
  T2               0                24
  T3               4               143
  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     2   2
  6Q GAIN WILD-TYPE  48 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    2
  6Q GAIN WILD-TYPE   48  127
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               2                48
  1               2               127
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  1
  6Q GAIN WILD-TYPE 84  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    1
  6Q GAIN WILD-TYPE   84    4
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               1                84
  1               1                 4
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  4
  6Q GAIN WILD-TYPE 82 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    4
  6Q GAIN WILD-TYPE   82   97
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               1                82
  MALE                 4                97
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3   2
  6Q GAIN WILD-TYPE 119  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    2
  6Q GAIN WILD-TYPE  119   40
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                3               119
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6Q GAIN MUTATED                                     3
  6Q GAIN WILD-TYPE                                 150
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6Q GAIN MUTATED                                       2
  6Q GAIN WILD-TYPE                                    23
                   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
D12V9, multiclass
                                                  clus
vv                                                 6Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 6Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            150
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           23
  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"
D12V10, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                55 
       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-HV-AA8V        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-7887        TCGA-IB-7891        TCGA-IB-8126 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V11, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                45 
       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-XN-A8T5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-YY-A8LH 
"6Q GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED     3   2   0   0
  6Q GAIN WILD-TYPE 108  51   5   4
D12V12, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               3               108
  R1               2                51
  R2               0                 5
  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"
D12V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         1     4
  6Q GAIN WILD-TYPE    11                         6   157
D12V14, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   4               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0   4
  6Q GAIN WILD-TYPE   5 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    4
  6Q GAIN WILD-TYPE    5  132
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4               132
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   24 28
  7P GAIN WILD-TYPE 62 68
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               52               130 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               28                68 
$`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        15.22        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        90.12        68.52        63.85 
TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAPZ 
       36.26        24.43         3.12        12.66        15.95        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-H8-A6C1 TCGA-HV-A5A6 
       15.55         4.04        24.36         5.10        22.06        66.94 
TCGA-HZ-7289 TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-HZ-A9TJ 
       21.73        17.03         3.95        17.92         5.26        19.82 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7893 
       49.38         4.77        23.80         4.04        15.81         3.85 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUQ TCGA-IB-AAUU 
       17.16        15.85         1.35         8.22         6.02         8.05 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-RB-A7B8 TCGA-S4-A8RM 
        9.14        12.92        12.46        19.20        15.32        24.23 
TCGA-US-A776 TCGA-US-A77E TCGA-YB-A89D TCGA-YY-A8LH 
       39.98        14.14        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        42.31        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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        50.70        32.81        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         9.50 
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 
       16.37         0.03        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-HV-A5A3 
       20.35        15.78        17.79        12.89        13.84         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
        7.63         9.50         8.28        32.15        30.25        17.49 
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        19.59         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-A5SQ 
       19.66        21.30        15.98         2.47        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-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV 
        7.86        14.17        11.11         7.40         9.44        13.28 
TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        10.29         8.78        15.45        13.68         3.12 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 
        9.40         0.30        17.26        23.08        22.85        16.80 
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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        12.76        15.35 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.35              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            90.12             75.12 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            15.68             14.70 
[1] "1.4 - 90.1 (15.7)" "0.0 - 75.1 (14.7)"
[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        37         0
  7P GAIN WILD-TYPE       0        5       12        22        84         5
                   vv
clus                STAGE IV
  7P GAIN MUTATED          2
  7P GAIN WILD-TYPE        3
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 5
  STAGE IB                3                12
  STAGE IIA               8                22
  STAGE IIB              37                84
  STAGE III               0                 5
  STAGE IV                2                 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  45   0
  7P GAIN WILD-TYPE   6  19 102   4
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               1                 6
  T2               5                19
  T3              45               102
  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   12 37
  7P GAIN WILD-TYPE 38 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     12   37
  7P GAIN WILD-TYPE   38   92
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              12                38
  1              37                92
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   23  2
  7P GAIN WILD-TYPE 62  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     23    2
  7P GAIN WILD-TYPE   62    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              23                62
  1               2                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   20 32
  7P GAIN WILD-TYPE 63 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     20   32
  7P GAIN WILD-TYPE   63   69
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              20                63
  MALE                32                69
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   39  9
  7P GAIN WILD-TYPE 83 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     39    9
  7P GAIN WILD-TYPE   83   33
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               39                83
  YES               9                33
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  7P GAIN MUTATED                                    38
  7P GAIN WILD-TYPE                                 115
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  7P GAIN MUTATED                                      12
  7P GAIN WILD-TYPE                                    13
                   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
D13V9, multiclass
                                                  clus
vv                                                 7P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           38
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 7P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D13V10, continuous
D13V11, continuous
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   27 18  1  3
  7P GAIN WILD-TYPE 84 35  4  1
D13V12, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              27                84
  R1              18                35
  R2               1                 4
  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"
D13V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       2                         3    44
  7P GAIN WILD-TYPE     9                         4   117
D13V14, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   2                 9
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  44               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"
D13V15, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    0 38
  7P GAIN WILD-TYPE  5 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0   38
  7P GAIN WILD-TYPE    5   98
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              38                98
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   20 28
  7Q GAIN WILD-TYPE 66 68
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48               134 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               28                68 
$`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        15.22        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        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPP 
       63.85        36.26        24.43         3.12        12.66        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-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 
        3.95        17.92         5.26        19.82        49.38         4.77 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A6UG 
       23.80         4.04        15.81         3.85        17.16         1.35 
TCGA-IB-A7LX TCGA-IB-AAUQ TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        8.22         6.02         8.05         9.14        12.92        12.46 
TCGA-M8-A5N4 TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-US-A776 TCGA-US-A77E TCGA-YB-A89D 
       19.20        15.32        24.23        39.98        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        42.31        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        58.98        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       24.26        33.57        50.70        32.81        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         9.50        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        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP 
        4.21         7.63         9.50        66.94         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       30.25        17.49         0.92        19.50         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
        0.26        27.62        20.19        23.21        12.03        19.59 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93         4.96        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
       10.13         6.38        21.60        10.85         1.08         0.23 
TCGA-IB-7644 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 
       12.95        21.90        15.35        19.82        15.65        41.33 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 
        3.62        43.79        19.66        21.30        15.98         2.47 
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-AAUO TCGA-IB-AAUP TCGA-IB-AAUR 
       15.88         0.26         4.73         7.86        14.17        11.11 
TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40         9.44        13.28         7.56        10.29         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RO 
       15.45        13.68         3.12         9.40         0.30        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       23.08        22.85        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       12.99        12.03        16.37        31.27        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.35              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            90.12             75.12 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            15.27             15.09 
[1] "1.4 - 90.1 (15.3)" "0.0 - 75.1 (15.1)"
[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        5       12        23        87         5
                   vv
clus                STAGE IV
  7Q GAIN MUTATED          2
  7Q GAIN WILD-TYPE        3
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 5
  STAGE IB                3                12
  STAGE IIA               7                23
  STAGE IIB              34                87
  STAGE III               0                 5
  STAGE IV                2                 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  42   0
  7Q GAIN WILD-TYPE   6  20 105   4
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               1                 6
  T2               4                20
  T3              42               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"
D14V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   11 34
  7Q GAIN WILD-TYPE 39 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     11   34
  7Q GAIN WILD-TYPE   39   95
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              11                39
  1              34                95
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   21  2
  7Q GAIN WILD-TYPE 64  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     21    2
  7Q GAIN WILD-TYPE   64    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              21                64
  1               2                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   18 30
  7Q GAIN WILD-TYPE 65 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     18   30
  7Q GAIN WILD-TYPE   65   71
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              18                65
  MALE                30                71
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   35  9
  7Q GAIN WILD-TYPE 87 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     35    9
  7Q GAIN WILD-TYPE   87   33
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               35                87
  YES               9                33
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  7Q GAIN MUTATED                                    35
  7Q GAIN WILD-TYPE                                 118
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  7Q GAIN MUTATED                                      11
  7Q GAIN WILD-TYPE                                    14
                   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
D14V9, multiclass
                                                  clus
vv                                                 7Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           35
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 7Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            118
  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"
D14V10, continuous
D14V11, continuous
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   24 17  1  3
  7Q GAIN WILD-TYPE 87 36  4  1
D14V12, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              24                87
  R1              17                36
  R2               1                 4
  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"
D14V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       1                         3    41
  7Q GAIN WILD-TYPE    10                         4   120
D14V14, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  41               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     0  36
  7Q GAIN WILD-TYPE   5 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0   36
  7Q GAIN WILD-TYPE    5  100
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              36               100
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   15 10
  8P GAIN WILD-TYPE 71 86
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25               157 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10                86 
$`8P GAIN MUTATED`
TCGA-2J-AABF TCGA-2J-AABH TCGA-3A-A9I5 TCGA-3A-A9IO TCGA-3A-A9IS TCGA-FB-A545 
       22.72        42.31        58.98        63.85        32.81        12.66 
TCGA-FB-AAPP TCGA-FB-AAQ1 TCGA-FZ-5921 TCGA-HV-AA8V TCGA-HZ-7922 TCGA-HZ-8315 
       15.95         4.04         5.10        30.25         0.13         9.83 
TCGA-HZ-A77O TCGA-IB-7646 TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-A5SP TCGA-IB-A6UF 
        5.26         4.77         4.04         3.85        15.85        21.90 
TCGA-IB-A6UG TCGA-M8-A5N4 TCGA-S4-A8RM TCGA-S4-A8RO TCGA-XN-A8T3 TCGA-YB-A89D 
        1.35        19.20        24.23        17.26        31.27        11.51 
TCGA-YH-A8SY 
       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        15.22        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        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IR 
       24.26        33.57        60.95        90.12        68.52        50.70 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       32.15        17.49        21.73         0.92        19.50         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-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
       19.59         3.95        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-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
        1.08         0.23        19.82        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-7897 TCGA-IB-8126 
       43.79        15.81        19.66        21.30        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7LX 
       17.16        12.00         7.20        15.12        20.88         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-OE-A75W TCGA-PZ-A5RE 
        9.14        12.92        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-A8RP 
       13.68         3.12        15.32         9.40         0.30        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        39.98        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YY-A8LH 
       13.81        12.99        12.03        16.37        23.67        66.28 
TCGA-Z5-AAPL 
       15.35 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.13              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            63.85             90.12 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            15.85             15.12 
[1] "0.1 - 63.9 (15.8)" "0.0 - 90.1 (15.1)"
[1] "hr=" "1.4"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  8P GAIN MUTATED         0        0        2         5        16         1
  8P GAIN WILD-TYPE       1        5       13        25       105         4
                   vv
clus                STAGE IV
  8P GAIN MUTATED          0
  8P GAIN WILD-TYPE        5
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                2                13
  STAGE IIA               5                25
  STAGE IIB              16               105
  STAGE III               1                 4
  STAGE IV                0                 5
[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     0   3  21   0
  8P GAIN WILD-TYPE   7  21 126   4
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               0                 7
  T2               3                21
  T3              21               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"
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     8  17
  8P GAIN WILD-TYPE  42 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      8   17
  8P GAIN WILD-TYPE   42  112
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               8                42
  1              17               112
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   12  0
  8P GAIN WILD-TYPE 73  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     12    0
  8P GAIN WILD-TYPE   73    5
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              12                73
  1               0                 5
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    9 17
  8P GAIN WILD-TYPE 74 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   17
  8P GAIN WILD-TYPE   74   84
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               9                74
  MALE                17                84
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    13  10
  8P GAIN WILD-TYPE 109  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     13   10
  8P GAIN WILD-TYPE  109   32
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               13               109
  YES              10                32
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8P GAIN MUTATED                                    22
  8P GAIN WILD-TYPE                                 131
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8P GAIN MUTATED                                       3
  8P GAIN WILD-TYPE                                    22
                   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
D15V9, multiclass
                                                  clus
vv                                                 8P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           22
  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                            131
  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"
D15V10, continuous
D15V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    11  11   1   0
  8P GAIN WILD-TYPE 100  42   4   4
D15V12, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              11               100
  R1              11                42
  R2               1                 4
  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"
D15V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       1                         0    23
  8P GAIN WILD-TYPE    10                         7   138
D15V14, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  23               138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  18
  8P GAIN WILD-TYPE   3 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   18
  8P GAIN WILD-TYPE    3  118
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              18               118
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   21 26
  8Q GAIN WILD-TYPE 65 70
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               47               135 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               26                70 
$`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        42.31        15.22         3.39        12.95 
TCGA-3A-A9I5 TCGA-3A-A9IB TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IX TCGA-3A-A9IZ 
       58.98         7.36        63.85        32.81        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        12.66         0.03        15.95        12.53 
TCGA-FB-AAQ1 TCGA-FZ-5921 TCGA-FZ-5926 TCGA-HV-A5A6 TCGA-HV-AA8V TCGA-HZ-7922 
        4.04         5.10        17.79        66.94        30.25         0.13 
TCGA-HZ-7925 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7646 
       20.19         9.83        17.92         5.26         0.23         4.77 
TCGA-IB-7647 TCGA-IB-7886 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP 
       21.90         4.04        19.66         3.85        17.16        15.85 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W 
       21.90         1.35         8.22         9.14        19.20         8.78 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY 
       24.23        17.26        31.27        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        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
       20.84        24.26        33.57        60.95        90.12        68.52 
TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       50.70        15.06        36.26        24.43        75.12        71.74 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN 
        9.50        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        16.37        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-A7OP 
       22.06         4.21         7.63         9.50         8.28        32.15 
TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        6.38        21.60        10.85         1.08        19.82        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-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 
        3.62        43.79        15.81        21.30        15.98         2.47 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUM 
       12.00         7.20        15.12        20.88        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-LB-A7SX TCGA-LB-A8F3 
        9.44         8.05        13.28         7.56        12.92        12.46 
TCGA-LB-A9Q5 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29        15.45        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
        0.30        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T5 TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        66.28        15.35 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.03              0.26 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            66.94             90.12 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.95             15.32 
[1] "0.0 - 66.9 (12.9)" "0.3 - 90.1 (15.3)"
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  8Q GAIN MUTATED         0        1        4         7        30         3
  8Q GAIN WILD-TYPE       1        4       11        23        91         2
                   vv
clus                STAGE IV
  8Q GAIN MUTATED          1
  8Q GAIN WILD-TYPE        4
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 4
  STAGE IB                4                11
  STAGE IIA               7                23
  STAGE IIB              30                91
  STAGE III               3                 2
  STAGE IV                1                 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 GAIN MUTATED     1   6  38   1
  8Q GAIN WILD-TYPE   6  18 109   3
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               1                 6
  T2               6                18
  T3              38               109
  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   15 32
  8Q GAIN WILD-TYPE 35 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     15   32
  8Q GAIN WILD-TYPE   35   97
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              15                35
  1              32                97
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   24  1
  8Q GAIN WILD-TYPE 61  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     24    1
  8Q GAIN WILD-TYPE   61    4
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              24                61
  1               1                 4
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   18 30
  8Q GAIN WILD-TYPE 65 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     18   30
  8Q GAIN WILD-TYPE   65   71
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              18                65
  MALE                30                71
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   30 12
  8Q GAIN WILD-TYPE 92 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     30   12
  8Q GAIN WILD-TYPE   92   30
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               30                92
  YES              12                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8Q GAIN MUTATED                                    41
  8Q GAIN WILD-TYPE                                 112
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8Q GAIN MUTATED                                       5
  8Q GAIN WILD-TYPE                                    20
                   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
D16V9, multiclass
                                                  clus
vv                                                 8Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           41
  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                            112
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           20
  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"
D16V10, continuous
D16V11, continuous
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   24 19  2  0
  8Q GAIN WILD-TYPE 87 34  3  4
D16V12, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              24                87
  R1              19                34
  R2               2                 3
  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"
D16V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       3                         0    42
  8Q GAIN WILD-TYPE     8                         7   119
D16V14, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   3                 8
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  42               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"
D16V15, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3  31
  8Q GAIN WILD-TYPE   2 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3   31
  8Q GAIN WILD-TYPE    2  105
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              31               105
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    5  3
  9P GAIN WILD-TYPE 81 93
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8               174 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                93 
$`9P GAIN MUTATED`
TCGA-2J-AABP TCGA-2L-AAQM TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-IB-7646 TCGA-IB-7893 
       15.22        45.47        15.95        23.54         4.77         3.85 
TCGA-M8-A5N4 TCGA-XN-A8T3 
       19.20        31.27 

$`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        42.31        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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        33.57        60.95        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP 
        4.21         7.63         9.50        66.94         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       19.66        21.30        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-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-A779 
       24.23        17.26        23.08        22.85        39.98        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-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       16.37        23.67        11.51        12.76        66.28        15.35 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             3.85              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            45.47             90.12 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           17.575            14.995 
[1] "3.9 - 45.5 (17.6)" "0.0 - 90.1 (15.0)"
[1] "hr=" "1.7"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  9P GAIN MUTATED         0        0        1         2         5         0
  9P GAIN WILD-TYPE       1        5       14        28       116         5
                   vv
clus                STAGE IV
  9P GAIN MUTATED          0
  9P GAIN WILD-TYPE        5
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               2                28
  STAGE IIB               5               116
  STAGE III               0                 5
  STAGE IV                0                 5
[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   2   6   0
  9P GAIN WILD-TYPE   7  22 141   4
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               0                 7
  T2               2                22
  T3               6               141
  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     3   5
  9P GAIN WILD-TYPE  47 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    5
  9P GAIN WILD-TYPE   47  124
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               3                47
  1               5               124
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    5  0
  9P GAIN WILD-TYPE 80  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    0
  9P GAIN WILD-TYPE   80    5
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               5                80
  1               0                 5
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  6
  9P GAIN WILD-TYPE 81 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    6
  9P GAIN WILD-TYPE   81   95
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                81
  MALE                 6                95
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     5   3
  9P GAIN WILD-TYPE 117  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    3
  9P GAIN WILD-TYPE  117   39
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                5               117
  YES               3                39
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9P GAIN MUTATED                                     6
  9P GAIN WILD-TYPE                                 147
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9P GAIN MUTATED                                       1
  9P GAIN WILD-TYPE                                    24
                   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
D17V9, multiclass
                                                  clus
vv                                                 9P 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                                                 9P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            147
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           24
  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"
D17V10, continuous
D17V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED     4   4   0   0
  9P GAIN WILD-TYPE 107  49   5   4
D17V12, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               4               107
  R1               4                49
  R2               0                 5
  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"
D17V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         0     7
  9P GAIN WILD-TYPE    11                         7   154
D17V14, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   7               154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1   4
  9P GAIN WILD-TYPE   4 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    4
  9P GAIN WILD-TYPE    4  132
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               4               132
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    7  5
  9Q GAIN WILD-TYPE 79 91
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               170 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                91 
$`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        36.26        15.95        23.54 
TCGA-IB-7646 TCGA-IB-7893 TCGA-IB-A5SP TCGA-M8-A5N4 TCGA-US-A779 TCGA-XN-A8T3 
        4.77         3.85        15.85        19.20        16.80        31.27 

$`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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IO 
        7.36        24.26        33.57        60.95        90.12        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        15.06        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.50        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
        9.50        66.94         8.28        32.15        30.25        17.49 
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        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98         2.47        17.16        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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       22.85        39.98        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        16.37        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             3.85              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            68.52             90.12 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             18.0              14.7 
[1] "3.9 - 68.5 (18.0)" "0.0 - 90.1 (14.7)"
[1] "hr=" "1.7"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  9Q GAIN MUTATED         0        0        3         3         6         0
  9Q GAIN WILD-TYPE       1        5       12        27       115         5
                   vv
clus                STAGE IV
  9Q GAIN MUTATED          0
  9Q GAIN WILD-TYPE        5
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                3                12
  STAGE IIA               3                27
  STAGE IIB               6               115
  STAGE III               0                 5
  STAGE IV                0                 5
[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   4   8   0
  9Q GAIN WILD-TYPE   7  20 139   4
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               0                 7
  T2               4                20
  T3               8               139
  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     5   6
  9Q GAIN WILD-TYPE  45 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    6
  9Q GAIN WILD-TYPE   45  123
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               5                45
  1               6               123
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    5  0
  9Q GAIN WILD-TYPE 80  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    0
  9Q GAIN WILD-TYPE   80    5
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               5                80
  1               0                 5
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  8
  9Q GAIN WILD-TYPE 79 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    8
  9Q GAIN WILD-TYPE   79   93
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               4                79
  MALE                 8                93
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     7   4
  9Q GAIN WILD-TYPE 115  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      7    4
  9Q GAIN WILD-TYPE  115   38
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                7               115
  YES               4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9Q GAIN MUTATED                                     9
  9Q GAIN WILD-TYPE                                 144
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9Q GAIN MUTATED                                       3
  9Q GAIN WILD-TYPE                                    22
                   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
D18V9, multiclass
                                                  clus
vv                                                 9Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            9
  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                            144
  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"
D18V10, continuous
D18V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED     5   6   0   1
  9Q GAIN WILD-TYPE 106  47   5   3
D18V12, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               5               106
  R1               6                47
  R2               0                 5
  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"
D18V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         0    11
  9Q GAIN WILD-TYPE    11                         7   150
D18V14, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  11               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"
D18V15, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1   7
  9Q GAIN WILD-TYPE   4 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    7
  9Q GAIN WILD-TYPE    4  129
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               7               129
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    6  4
  10P GAIN WILD-TYPE 80 92
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                172 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 92 
$`10P GAIN MUTATED`
TCGA-2L-AAQL TCGA-3A-A9IO TCGA-F2-A7TX TCGA-FZ-5920 TCGA-HV-A7OP TCGA-HZ-A9TJ 
        9.60        63.85         3.12         2.01        32.15        19.82 
TCGA-IB-A5SP TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       15.85         8.05        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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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 
       12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       17.49        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 
       19.59         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-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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        39.98        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              2.01               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             63.85              90.12 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             12.69              15.27 
[1] "2.0 - 63.9 (12.7)" "0.0 - 90.1 (15.3)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  10P GAIN MUTATED         0        0        0         2         6         0
  10P GAIN WILD-TYPE       1        5       15        28       115         5
                    vv
clus                 STAGE IV
  10P GAIN MUTATED          1
  10P GAIN WILD-TYPE        4
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 0                 15
  STAGE IIA                2                 28
  STAGE IIB                6                115
  STAGE III                0                  5
  STAGE IV                 1                  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   9   0
  10P GAIN WILD-TYPE   7  24 138   4
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  7
  T2                0                 24
  T3                9                138
  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     3   6
  10P GAIN WILD-TYPE  47 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    6
  10P GAIN WILD-TYPE   47  123
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                3                 47
  1                6                123
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    5  1
  10P GAIN WILD-TYPE 80  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    1
  10P GAIN WILD-TYPE   80    4
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                5                 80
  1                1                  4
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  8
  10P GAIN WILD-TYPE 81 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    8
  10P GAIN WILD-TYPE   81   93
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                2                 81
  MALE                  8                 93
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     8   2
  10P GAIN WILD-TYPE 114  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    2
  10P GAIN WILD-TYPE  114   40
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 8                114
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10P GAIN MUTATED                                     7
  10P GAIN WILD-TYPE                                 146
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10P GAIN MUTATED                                       3
  10P GAIN WILD-TYPE                                    22
                    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
D19V9, multiclass
                                                  clus
vv                                                 10P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 10P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             146
  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"
D19V10, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 54 
        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-HV-AA8V         TCGA-HZ-A77Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7887         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-S4-A8RP         TCGA-US-A774 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-XN-A8T5         TCGA-YY-A8LH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D19V11, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 45 
        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-XN-A8T5         TCGA-YY-A8LH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED     6   3   0   1
  10P GAIN WILD-TYPE 105  50   5   3
D19V12, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                6                105
  R1                3                 50
  R2                0                  5
  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"
D19V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       1                         3     6
  10P GAIN WILD-TYPE    10                         4   155
D19V14, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                3                  4
  WHITE                                    6                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"
D19V15, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0   6
  10P GAIN WILD-TYPE   5 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    6
  10P GAIN WILD-TYPE    5  130
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                6                130
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    5  8
  10Q GAIN WILD-TYPE 81 88
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                169 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                 88 
$`10Q GAIN MUTATED`
TCGA-2L-AAQL TCGA-3A-A9IO TCGA-F2-A7TX TCGA-FZ-5920 TCGA-FZ-5923 TCGA-HV-A7OP 
        9.60        63.85         3.12         2.01        20.35        32.15 
TCGA-IB-7886 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUU TCGA-LB-A7SX 
        4.04        15.85         1.35         8.22         8.05        12.92 
TCGA-LB-A8F3 
       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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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 
       12.66        16.37         0.03        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-HV-A5A3 
       15.78        17.79        12.89        13.84        22.06         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
        7.63         9.50        66.94         8.28        30.25        17.49 
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        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-A5SQ 
        3.85        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-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
       13.28         7.56         9.14        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 
       24.23        17.26        23.08        22.85        39.98        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.35               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             63.85              90.12 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              9.60              15.35 
[1] "1.4 - 63.9 (9.6)"  "0.0 - 90.1 (15.3)"
[1] "hr=" "1.7"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  10Q GAIN MUTATED         0        0        0         2         9         0
  10Q GAIN WILD-TYPE       1        5       15        28       112         5
                    vv
clus                 STAGE IV
  10Q GAIN MUTATED          1
  10Q GAIN WILD-TYPE        4
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 0                 15
  STAGE IIA                2                 28
  STAGE IIB                9                112
  STAGE III                0                  5
  STAGE IV                 1                  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
  10Q GAIN MUTATED     0   0  11   1
  10Q GAIN WILD-TYPE   7  24 136   3
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  7
  T2                0                 24
  T3               11                136
  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  10
  10Q GAIN WILD-TYPE  48 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   10
  10Q GAIN WILD-TYPE   48  119
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                2                 48
  1               10                119
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    7  1
  10Q GAIN WILD-TYPE 78  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7    1
  10Q GAIN WILD-TYPE   78    4
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                7                 78
  1                1                  4
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2 11
  10Q GAIN WILD-TYPE 81 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   11
  10Q GAIN WILD-TYPE   81   90
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                 81
  MALE                 11                 90
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    11   2
  10Q GAIN WILD-TYPE 111  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     11    2
  10Q GAIN WILD-TYPE  111   40
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                11                111
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10Q GAIN MUTATED                                    11
  10Q GAIN WILD-TYPE                                 142
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10Q GAIN MUTATED                                       2
  10Q GAIN WILD-TYPE                                    23
                    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
D20V9, multiclass
                                                  clus
vv                                                 10Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 10Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             142
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            23
  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"
D20V10, continuous
D20V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     7   5   0   1
  10Q GAIN WILD-TYPE 104  48   5   3
D20V12, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                7                104
  R1                5                 48
  R2                0                  5
  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"
D20V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       1                         3     9
  10Q GAIN WILD-TYPE    10                         4   152
D20V14, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                3                  4
  WHITE                                    9                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"
D20V15, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   9
  10Q GAIN WILD-TYPE   5 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    9
  10Q GAIN WILD-TYPE    5  127
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                9                127
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    6  7
  11P GAIN WILD-TYPE 80 89
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                169 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                 89 
$`11P GAIN MUTATED`
TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-HZ-A4BH TCGA-IB-7647 
        3.12        12.66        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 
       39.98 

$`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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       43.50        20.84         7.36        24.26        33.57        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       90.12        68.52        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.50        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        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP 
        4.21         7.63         9.50        66.94         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       30.25        17.49        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        19.59         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-A4BK 
       17.92         4.96        21.70        16.14        10.13        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
       49.38         4.77        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-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-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-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        24.23        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.35               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             39.98              90.12 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             12.66              15.22 
[1] "1.4 - 40.0 (12.7)" "0.0 - 90.1 (15.2)"
[1] "hr=" "1.5"
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        5       15        25       113         5
                    vv
clus                 STAGE IV
  11P GAIN MUTATED          0
  11P GAIN WILD-TYPE        5
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 0                 15
  STAGE IIA                5                 25
  STAGE IIB                8                113
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   7  24 134   4
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                0                  7
  T2                0                 24
  T3               13                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"
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5   8
  11P GAIN WILD-TYPE  45 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    8
  11P GAIN WILD-TYPE   45  121
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                5                 45
  1                8                121
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    8  0
  11P GAIN WILD-TYPE 77  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    0
  11P GAIN WILD-TYPE   77    5
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                8                 77
  1                0                  5
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2 11
  11P GAIN WILD-TYPE 81 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   11
  11P GAIN WILD-TYPE   81   90
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 81
  MALE                 11                 90
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    10   2
  11P GAIN WILD-TYPE 112  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10    2
  11P GAIN WILD-TYPE  112   40
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                10                112
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11P GAIN MUTATED                                    12
  11P GAIN WILD-TYPE                                 141
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11P GAIN MUTATED                                       0
  11P GAIN WILD-TYPE                                    25
                    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
D21V9, 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                             141
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            25
  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"
D21V10, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 54 
        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-HV-AA8V         TCGA-HZ-A77Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7887         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-AAUU         TCGA-IB-AAUV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-XN-A8T5         TCGA-YY-A8LH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V11, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 44 
        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-XN-A8T5         TCGA-YY-A8LH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED     4   8   0   0
  11P GAIN WILD-TYPE 107  45   5   4
D21V12, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                4                107
  R1                8                 45
  R2                0                  5
  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"
D21V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0    12
  11P GAIN WILD-TYPE    11                         7   149
D21V14, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   12                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"
D21V15, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0   9
  11P GAIN WILD-TYPE   5 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    9
  11P GAIN WILD-TYPE    5  127
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                9                127
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    4 10
  11Q GAIN WILD-TYPE 82 86
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                168 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                 86 
$`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        12.66        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        42.31        31.86        15.91        14.47        15.22 
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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       34.09        24.43        75.12        71.74        10.98         9.50 
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 
       16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
       12.89        13.84        22.06         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 
       66.94         8.28        32.15        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        1.08         0.23        19.82        12.95        49.38         4.77 
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-7897 TCGA-IB-8126 
       43.79        15.81        19.66        21.30        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-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE 
        9.14        12.92        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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.35               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             23.54              90.12 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             9.880             15.335 
[1] "1.4 - 23.5 (9.9)"  "0.0 - 90.1 (15.3)"
[1] "hr=" "2.3"
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        5       15        25       111         5
                    vv
clus                 STAGE IV
  11Q GAIN MUTATED          0
  11Q GAIN WILD-TYPE        5
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 0                 15
  STAGE IIA                5                 25
  STAGE IIB               10                111
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   7  23 133   4
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                0                  7
  T2                1                 23
  T3               14                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"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     5  10
  11Q GAIN WILD-TYPE  45 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5   10
  11Q GAIN WILD-TYPE   45  119
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                5                 45
  1               10                119
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    9  0
  11Q GAIN WILD-TYPE 76  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      9    0
  11Q GAIN WILD-TYPE   76    5
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                9                 76
  1                0                  5
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3 12
  11Q GAIN WILD-TYPE 80 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   12
  11Q GAIN WILD-TYPE   80   89
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 80
  MALE                 12                 89
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    12   2
  11Q GAIN WILD-TYPE 110  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12    2
  11Q GAIN WILD-TYPE  110   40
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                12                110
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11Q GAIN MUTATED                                    15
  11Q GAIN WILD-TYPE                                 138
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11Q GAIN MUTATED                                       0
  11Q GAIN WILD-TYPE                                    25
                    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
D22V9, 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                             138
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            25
  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"
D22V10, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 54 
        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-HV-AA8V         TCGA-HZ-A77Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-7887         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-AAUU         TCGA-IB-AAUV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-XN-A8T5         TCGA-YY-A8LH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V11, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 44 
        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-XN-A8T5         TCGA-YY-A8LH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED     6   8   0   0
  11Q GAIN WILD-TYPE 105  45   5   4
D22V12, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                6                105
  R1                8                 45
  R2                0                  5
  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"
D22V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0    14
  11Q GAIN WILD-TYPE    11                         7   147
D22V14, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   14                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"
D22V15, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     2   9
  11Q GAIN WILD-TYPE   3 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    9
  11Q GAIN WILD-TYPE    3  127
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO                9                127
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   13 17
  12P GAIN WILD-TYPE 73 79
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                30                152 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                17                 79 
$`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        58.98         7.36 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IV TCGA-F2-A7TX 
       90.12        68.52        63.85        32.81        36.26         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-HV-A5A3 TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-HZ-A77O TCGA-HZ-A9TJ 
        4.21        21.73         0.13         3.95         5.26        19.82 
TCGA-IB-7646 TCGA-IB-7890 TCGA-IB-A6UG TCGA-IB-A7LX TCGA-Q3-AA2A TCGA-YH-A8SY 
        4.77        19.66         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        42.31        15.91        14.47        15.22        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        43.50        20.84        24.26        33.57        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        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        12.66        16.37         0.03 
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-HV-A5A4 TCGA-HV-A5A5 
       17.79        12.89        13.84        22.06         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       66.94         8.28        32.15        30.25        17.49         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-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03        19.59         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-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
       21.60        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-7891 TCGA-IB-7893 
        4.04         3.62        43.79        15.81        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-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-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-RB-A7B8 
       10.29        19.20         8.78        15.45        13.68        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
        9.40         0.30        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       39.98        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.13               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             90.12              75.12 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            15.665             15.090 
[1] "0.1 - 90.1 (15.7)" "0.0 - 75.1 (15.1)"
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  12P GAIN MUTATED         1        0        5         4        16         1
  12P GAIN WILD-TYPE       0        5       10        26       105         4
                    vv
clus                 STAGE IV
  12P GAIN MUTATED          1
  12P GAIN WILD-TYPE        4
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 5                 10
  STAGE IIA                4                 26
  STAGE IIB               16                105
  STAGE III                1                  4
  STAGE IV                 1                  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     1   6  21   0
  12P GAIN WILD-TYPE   6  18 126   4
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                1                  6
  T2                6                 18
  T3               21                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"
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7  19
  12P GAIN WILD-TYPE  43 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7   19
  12P GAIN WILD-TYPE   43  110
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                7                 43
  1               19                110
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    7  1
  12P GAIN WILD-TYPE 78  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7    1
  12P GAIN WILD-TYPE   78    4
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                7                 78
  1                1                  4
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   10 20
  12P GAIN WILD-TYPE 73 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10   20
  12P GAIN WILD-TYPE   73   81
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               10                 73
  MALE                 20                 81
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   23  6
  12P GAIN WILD-TYPE 99 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     23    6
  12P GAIN WILD-TYPE   99   36
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                23                 99
  YES                6                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12P GAIN MUTATED                                    20
  12P GAIN WILD-TYPE                                 133
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12P GAIN MUTATED                                       9
  12P GAIN WILD-TYPE                                    16
                    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
D23V9, multiclass
                                                  clus
vv                                                 12P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            20
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 12P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             133
  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"
D23V10, continuous
D23V11, continuous
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED   16  9  0  3
  12P GAIN WILD-TYPE 95 44  5  1
D23V12, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               16                 95
  R1                9                 44
  R2                0                  5
  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"
D23V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       1                         0    28
  12P GAIN WILD-TYPE    10                         7   133
D23V14, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   28                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"
D23V15, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  23
  12P GAIN WILD-TYPE   5 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   23
  12P GAIN WILD-TYPE    5  113
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               23                113
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   10 12
  12Q GAIN WILD-TYPE 76 84
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                22                160 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                12                 84 
$`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        58.98         7.36        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-AAPP TCGA-FB-AAPZ 
       63.85        32.81        36.26         3.12        15.95        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-HV-A5A3 TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-8005 
       15.55         4.04         4.21        21.73         0.13         3.95 
TCGA-IB-7646 TCGA-IB-A6UG TCGA-IB-A7LX TCGA-Q3-AA2A 
        4.77         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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       33.57        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 
       24.43        75.12        71.74        10.98         9.50        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37         0.03        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-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84        22.06         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       32.15        30.25        17.49         0.92        19.50         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-8636 TCGA-HZ-8638 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-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-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-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.32         9.40         0.30        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        39.98        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.13               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             90.12              75.12 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            12.575             15.170 
[1] "0.1 - 90.1 (12.6)" "0.0 - 75.1 (15.2)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  12Q GAIN MUTATED         1        0        4         2        13         0
  12Q GAIN WILD-TYPE       0        5       11        28       108         5
                    vv
clus                 STAGE IV
  12Q GAIN MUTATED          0
  12Q GAIN WILD-TYPE        5
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 4                 11
  STAGE IIA                2                 28
  STAGE IIB               13                108
  STAGE III                0                  5
  STAGE IV                 0                  5
[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     1   4  15   0
  12Q GAIN WILD-TYPE   6  20 132   4
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                1                  6
  T2                4                 20
  T3               15                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"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4  14
  12Q GAIN WILD-TYPE  46 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4   14
  12Q GAIN WILD-TYPE   46  115
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                4                 46
  1               14                115
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    3  0
  12Q GAIN WILD-TYPE 82  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    0
  12Q GAIN WILD-TYPE   82    5
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                3                 82
  1                0                  5
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    6 16
  12Q GAIN WILD-TYPE 77 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      6   16
  12Q GAIN WILD-TYPE   77   85
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                6                 77
  MALE                 16                 85
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    18   3
  12Q GAIN WILD-TYPE 104  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     18    3
  12Q GAIN WILD-TYPE  104   39
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                18                104
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12Q GAIN MUTATED                                    15
  12Q GAIN WILD-TYPE                                 138
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12Q GAIN MUTATED                                       7
  12Q GAIN WILD-TYPE                                    18
                    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
D24V9, multiclass
                                                  clus
vv                                                 12Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            15
  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                             138
  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"
D24V10, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 54 
        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-HV-AA8V         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7886 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7887         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-AAUU         TCGA-IB-AAUV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-XN-A8T5         TCGA-YY-A8LH 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D24V11, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 44 
        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-XN-A8T5         TCGA-YY-A8LH 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    11   7   0   3
  12Q GAIN WILD-TYPE 100  46   5   1
D24V12, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               11                100
  R1                7                 46
  R2                0                  5
  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"
D24V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       1                         0    21
  12Q GAIN WILD-TYPE    10                         7   140
D24V14, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   21                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"
D24V15, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  18
  12Q GAIN WILD-TYPE   5 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   18
  12Q GAIN WILD-TYPE    5  118
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               18                118
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   17 12
  13Q GAIN WILD-TYPE 69 84
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                29                153 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                12                 84 
$`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        42.31        15.22        10.49 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IV TCGA-3A-A9J0 
        9.60        45.47        90.12        63.85        36.26        24.43 
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-HV-A5A5 TCGA-HV-A7OP TCGA-HZ-7922 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ 
        9.50        32.15         0.13         5.26        10.85        19.82 
TCGA-IB-7645 TCGA-IB-A5SO TCGA-IB-A7LX TCGA-IB-AAUU TCGA-YB-A89D 
       49.38        12.00         8.22         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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IR 
        7.36        24.26        33.57        60.95        68.52        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       32.81        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         9.50        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        12.66        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 
       15.78        17.79        12.89        22.06         4.21         7.63 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 
       66.94         8.28        30.25        17.49        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        19.59         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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        39.98        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.13               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             90.12              75.12 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             12.00              15.35 
[1] "0.1 - 90.1 (12.0)" "0.0 - 75.1 (15.3)"
[1] "hr=" "1.5"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  13Q GAIN MUTATED         1        1        1         3        21         0
  13Q GAIN WILD-TYPE       0        4       14        27       100         5
                    vv
clus                 STAGE IV
  13Q GAIN MUTATED          1
  13Q GAIN WILD-TYPE        4
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 1                  4
  STAGE IB                 1                 14
  STAGE IIA                3                 27
  STAGE IIB               21                100
  STAGE III                0                  5
  STAGE IV                 1                  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  23   0
  13Q GAIN WILD-TYPE   5  21 124   4
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                2                  5
  T2                3                 21
  T3               23                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"
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     6  21
  13Q GAIN WILD-TYPE  44 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   21
  13Q GAIN WILD-TYPE   44  108
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                6                 44
  1               21                108
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   12  1
  13Q GAIN WILD-TYPE 73  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12    1
  13Q GAIN WILD-TYPE   73    4
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               12                 73
  1                1                  4
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   11 18
  13Q GAIN WILD-TYPE 72 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     11   18
  13Q GAIN WILD-TYPE   72   83
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               11                 72
  MALE                 18                 83
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    22   4
  13Q GAIN WILD-TYPE 100  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     22    4
  13Q GAIN WILD-TYPE  100   38
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                22                100
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  13Q GAIN MUTATED                                    19
  13Q GAIN WILD-TYPE                                 134
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  13Q GAIN MUTATED                                       9
  13Q GAIN WILD-TYPE                                    16
                    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
D25V9, multiclass
                                                  clus
vv                                                 13Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 13Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             134
  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"
D25V10, continuous
D25V11, continuous
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 45 
        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-XN-A8T5         TCGA-YY-A8LH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED   21  4  0  1
  13Q GAIN WILD-TYPE 90 49  5  3
D25V12, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               21                 90
  R1                4                 49
  R2                0                  5
  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"
D25V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       2                         0    25
  13Q GAIN WILD-TYPE     9                         7   136
D25V14, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    2                  9
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   25                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"
D25V15, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  16
  13Q GAIN WILD-TYPE   5 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   16
  13Q GAIN WILD-TYPE    5  120
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               16                120
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   16  9
  14Q GAIN WILD-TYPE 70 87
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                25                157 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                 87 
$`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 
       36.26         3.12        12.66        15.95        23.54         8.02 
TCGA-HV-A5A5 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-IB-7886 TCGA-IB-8127 
        9.50         0.13        17.92         6.38         4.04        17.16 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUU TCGA-M8-A5N4 TCGA-S4-A8RO 
        1.35         8.22        15.88         8.05        19.20        17.26 
TCGA-YB-A89D 
       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        42.31        31.86        15.91        15.22        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        58.98        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       33.57        60.95        90.12        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN 
        9.50        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        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 
       66.94         8.28        32.15        30.25        17.49        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        19.59         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-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
       19.66        21.30         3.85        15.98         2.47        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-AAUM 
       15.85         7.20        15.12        20.88        21.90         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-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-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40         0.30        24.23        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        16.37        31.27        23.67        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.13               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             68.52              90.12 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             12.66              15.32 
[1] "0.1 - 68.5 (12.7)" "0.0 - 90.1 (15.3)"
[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        19         0
  14Q GAIN WILD-TYPE       1        4       13        28       102         5
                    vv
clus                 STAGE IV
  14Q GAIN MUTATED          1
  14Q GAIN WILD-TYPE        4
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  4
  STAGE IB                 2                 13
  STAGE IIA                2                 28
  STAGE IIB               19                102
  STAGE III                0                  5
  STAGE IV                 1                  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 GAIN MUTATED     1   3  21   0
  14Q GAIN WILD-TYPE   6  21 126   4
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                  6
  T2                3                 21
  T3               21                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"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  19
  14Q GAIN WILD-TYPE  45 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   19
  14Q GAIN WILD-TYPE   45  110
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                5                 45
  1               19                110
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   10  1
  14Q GAIN WILD-TYPE 75  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10    1
  14Q GAIN WILD-TYPE   75    4
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               10                 75
  1                1                  4
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   10 16
  14Q GAIN WILD-TYPE 73 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10   16
  14Q GAIN WILD-TYPE   73   85
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               10                 73
  MALE                 16                 85
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15   7
  14Q GAIN WILD-TYPE 107  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15    7
  14Q GAIN WILD-TYPE  107   35
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                15                107
  YES                7                 35
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  14Q GAIN MUTATED                                    22
  14Q GAIN WILD-TYPE                                 131
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  14Q GAIN MUTATED                                       4
  14Q GAIN WILD-TYPE                                    21
                    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
D26V9, multiclass
                                                  clus
vv                                                 14Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            22
  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                             131
  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"
D26V10, continuous
D26V11, continuous
                    vv
clus                 R0 R1 R2 RX
  14Q GAIN MUTATED   14 10  0  0
  14Q GAIN WILD-TYPE 97 43  5  4
D26V12, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               14                 97
  R1               10                 43
  R2                0                  5
  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"
D26V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       1                         0    24
  14Q GAIN WILD-TYPE    10                         7   137
D26V14, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   24                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"
D26V15, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  18
  14Q GAIN WILD-TYPE   4 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   18
  14Q GAIN WILD-TYPE    4  118
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               18                118
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    7  7
  15Q GAIN WILD-TYPE 79 89
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                168 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                 89 
$`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        90.12        24.43         3.12         5.10 
TCGA-HV-A5A5 TCGA-HZ-7922 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-AAUU TCGA-RB-A7B8 
        9.50         0.13         4.04        15.81         8.05        15.32 
TCGA-S4-A8RP TCGA-US-A776 
       23.08        39.98 

$`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        42.31        31.86        15.91        15.22 
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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        24.26        33.57        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        32.81        15.06        36.26        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         9.50        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        12.66        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 
       66.94         8.28        32.15        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       43.79        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-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-AA9M 
       19.20         8.78        15.45        13.68         3.12         9.40 
TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E 
        0.30        24.23        17.26        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.13               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             90.12              75.12 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            12.035             15.285 
[1] "0.1 - 90.1 (12.0)" "0.0 - 75.1 (15.3)"
[1] "hr=" "1"  
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  15Q GAIN MUTATED         1        0        0         1        12         0
  15Q GAIN WILD-TYPE       0        5       15        29       109         5
                    vv
clus                 STAGE IV
  15Q GAIN MUTATED          0
  15Q GAIN WILD-TYPE        5
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 0                 15
  STAGE IIA                1                 29
  STAGE IIB               12                109
  STAGE III                0                  5
  STAGE IV                 0                  5
[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  13   0
  15Q GAIN WILD-TYPE   6  24 134   4
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                1                  6
  T2                0                 24
  T3               13                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"
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  12
  15Q GAIN WILD-TYPE  49 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   12
  15Q GAIN WILD-TYPE   49  117
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                1                 49
  1               12                117
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    7  0
  15Q GAIN WILD-TYPE 78  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7    0
  15Q GAIN WILD-TYPE   78    5
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                7                 78
  1                0                  5
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    7  7
  15Q GAIN WILD-TYPE 76 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7    7
  15Q GAIN WILD-TYPE   76   94
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                7                 76
  MALE                  7                 94
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    10   3
  15Q GAIN WILD-TYPE 112  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10    3
  15Q GAIN WILD-TYPE  112   39
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                10                112
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  15Q GAIN MUTATED                                    11
  15Q GAIN WILD-TYPE                                 142
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  15Q GAIN MUTATED                                       2
  15Q GAIN WILD-TYPE                                    23
                    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
D27V9, multiclass
                                                  clus
vv                                                 15Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  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                             142
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            23
  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"
D27V10, continuous
D27V11, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 44 
        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-XN-A8T5         TCGA-YY-A8LH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     9   2   0   1
  15Q GAIN WILD-TYPE 102  51   5   3
D27V12, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                9                102
  R1                2                 51
  R2                0                  5
  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"
D27V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         0    12
  15Q GAIN WILD-TYPE    10                         7   149
D27V14, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   12                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"
D27V15, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0   8
  15Q GAIN WILD-TYPE   5 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    8
  15Q GAIN WILD-TYPE    5  128
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                8                128
[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 78 82
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                160 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                14                 82 
$`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        24.43 
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 
       42.31        31.86        15.91        14.47        15.22        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        58.98        43.50        20.84        33.57 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        90.12        68.52        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        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         9.50        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        12.66        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       32.15        30.25        17.49         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        19.59         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-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        4.77        21.90        15.35        19.82        23.80        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-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22         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-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
        9.14        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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
       18.67        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        12.76        66.28        15.35 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              2.63               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             24.43              90.12 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            15.750             14.995 
[1] "2.6 - 24.4 (15.8)" "0.0 - 90.1 (15.0)"
[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        5       14        27       104         5
                    vv
clus                 STAGE IV
  16P GAIN MUTATED          1
  16P GAIN WILD-TYPE        4
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 1                 14
  STAGE IIA                3                 27
  STAGE IIB               17                104
  STAGE III                0                  5
  STAGE IV                 1                  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 GAIN MUTATED     0   3  19   0
  16P GAIN WILD-TYPE   7  21 128   4
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                0                  7
  T2                3                 21
  T3               19                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"
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     5  17
  16P GAIN WILD-TYPE  45 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   17
  16P GAIN WILD-TYPE   45  112
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                5                 45
  1               17                112
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    9  1
  16P GAIN WILD-TYPE 76  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    1
  16P GAIN WILD-TYPE   76    4
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                9                 76
  1                1                  4
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    6 16
  16P GAIN WILD-TYPE 77 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6   16
  16P GAIN WILD-TYPE   77   85
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                6                 77
  MALE                 16                 85
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    15   5
  16P GAIN WILD-TYPE 107  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     15    5
  16P GAIN WILD-TYPE  107   37
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                15                107
  YES                5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16P GAIN MUTATED                                    21
  16P GAIN WILD-TYPE                                 132
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16P GAIN MUTATED                                       1
  16P GAIN WILD-TYPE                                    24
                    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
D28V9, 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                             132
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            24
  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"
D28V10, continuous
D28V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    11   9   0   2
  16P GAIN WILD-TYPE 100  44   5   2
D28V12, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               11                100
  R1                9                 44
  R2                0                  5
  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"
D28V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       0                         1    19
  16P GAIN WILD-TYPE    11                         6   142
D28V14, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   19                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"
D28V15, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  16
  16P GAIN WILD-TYPE   5 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   16
  16P GAIN WILD-TYPE    5  120
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               16                120
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   12 11
  16Q GAIN WILD-TYPE 74 85
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                23                159 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                11                 85 
$`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        24.43        12.66        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-HZ-A9TJ TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7890 TCGA-IB-8127 TCGA-IB-A5SP 
       19.82        15.65         4.04        19.66        17.16        15.85 
TCGA-IB-A7M4 TCGA-IB-AAUU TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-YB-A89D 
       15.88         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 
       42.31        31.86        15.91        14.47        15.22        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        58.98        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        33.57        60.95        90.12        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        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         9.50        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        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       32.15        30.25        17.49        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        19.59         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-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-7885 TCGA-IB-7887 
       21.90        15.35        19.82        23.80        41.33         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       43.79        15.81        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-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22         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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        39.98        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              2.63               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             24.43              90.12 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             15.85              14.93 
[1] "2.6 - 24.4 (15.8)" "0.0 - 90.1 (14.9)"
[1] "hr=" "1"  
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        5       14        27       104         5
                    vv
clus                 STAGE IV
  16Q GAIN MUTATED          2
  16Q GAIN WILD-TYPE        3
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 1                 14
  STAGE IIA                3                 27
  STAGE IIB               17                104
  STAGE III                0                  5
  STAGE IV                 2                  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  19   0
  16Q GAIN WILD-TYPE   7  20 128   4
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                0                  7
  T2                4                 20
  T3               19                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"
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     6  17
  16Q GAIN WILD-TYPE  44 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6   17
  16Q GAIN WILD-TYPE   44  112
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                6                 44
  1               17                112
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   10  2
  16Q GAIN WILD-TYPE 75  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    2
  16Q GAIN WILD-TYPE   75    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               10                 75
  1                2                  3
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    6 17
  16Q GAIN WILD-TYPE 77 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6   17
  16Q GAIN WILD-TYPE   77   84
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                6                 77
  MALE                 17                 84
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    15   6
  16Q GAIN WILD-TYPE 107  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     15    6
  16Q GAIN WILD-TYPE  107   36
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                15                107
  YES                6                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16Q GAIN MUTATED                                    21
  16Q GAIN WILD-TYPE                                 132
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16Q GAIN MUTATED                                       2
  16Q GAIN WILD-TYPE                                    23
                    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
D29V9, multiclass
                                                  clus
vv                                                 16Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 16Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             132
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            23
  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"
D29V10, continuous
D29V11, continuous
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED   12 10  0  0
  16Q GAIN WILD-TYPE 99 43  5  4
D29V12, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               12                 99
  R1               10                 43
  R2                0                  5
  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"
D29V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         1    20
  16Q GAIN WILD-TYPE    11                         6   141
D29V14, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   20                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"
D29V15, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  18
  16Q GAIN WILD-TYPE   5 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   18
  16Q GAIN WILD-TYPE    5  118
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               18                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 78 95
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                173 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 95 
$`17P GAIN MUTATED`
TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       15.22        45.47        58.98        90.12        68.52        63.85 
TCGA-3A-A9IV TCGA-IB-7646 TCGA-LB-A8F3 
       36.26         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        42.31        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        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        60.95        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.50        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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
       12.89        13.84        22.06         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 
       66.94         8.28        32.15        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
        1.08         0.23        19.82        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-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-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
       12.92        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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
       18.67        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              4.77               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             90.12              75.12 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             45.47              14.93 
[1] "4.8 - 90.1 (45.5)" "0.0 - 75.1 (14.9)"
[1] "hr=" "11" 
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  17P GAIN MUTATED         1        0        2         1         3         0
  17P GAIN WILD-TYPE       0        5       13        29       118         5
                    vv
clus                 STAGE IV
  17P GAIN MUTATED          0
  17P GAIN WILD-TYPE        5
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA                1                 29
  STAGE IIB                3                118
  STAGE III                0                  5
  STAGE IV                 0                  5
[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     1   2   4   0
  17P GAIN WILD-TYPE   6  22 143   4
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                1                  6
  T2                2                 22
  T3                4                143
  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  47 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    3
  17P GAIN WILD-TYPE   47  126
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                3                 47
  1                3                126
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    2  0
  17P GAIN WILD-TYPE 83  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    0
  17P GAIN WILD-TYPE   83    5
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                2                 83
  1                0                  5
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  4
  17P GAIN WILD-TYPE 78 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    4
  17P GAIN WILD-TYPE   78   97
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                5                 78
  MALE                  4                 97
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     6   3
  17P GAIN WILD-TYPE 116  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6    3
  17P GAIN WILD-TYPE  116   39
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 6                116
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17P GAIN MUTATED                                     3
  17P GAIN WILD-TYPE                                 150
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17P GAIN MUTATED                                       5
  17P GAIN WILD-TYPE                                    20
                    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
D30V9, 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                             150
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            20
  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"
D30V10, continuous
D30V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     6   3   0   0
  17P GAIN WILD-TYPE 105  50   5   4
D30V12, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                6                105
  R1                3                 50
  R2                0                  5
  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"
D30V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       0                         1     8
  17P GAIN WILD-TYPE    11                         6   153
D30V14, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    8                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"
D30V15, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0   7
  17P GAIN WILD-TYPE   5 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    7
  17P GAIN WILD-TYPE    5  129
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                7                129
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   15  2
  17Q GAIN WILD-TYPE 71 94
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                165 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 94 
$`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        58.98        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IV TCGA-FB-A545 TCGA-FB-AAQ1 TCGA-HZ-7922 TCGA-HZ-A9TJ 
       63.85        36.26        12.66         4.04         0.13        19.82 
TCGA-IB-7646 TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-S4-A8RO 
        4.77        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        42.31        15.91        15.22        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        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       33.57        60.95        50.70        32.81        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP 
        4.21         7.63         9.50        66.94         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       30.25        17.49        21.73         0.92        19.50         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-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       19.59         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-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-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        24.23        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       39.98        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.13               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             90.12              75.12 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             19.20              14.93 
[1] "0.1 - 90.1 (19.2)" "0.0 - 75.1 (14.9)"
[1] "hr=" "7.6"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  17Q GAIN MUTATED         1        0        2         3         8         0
  17Q GAIN WILD-TYPE       0        5       13        27       113         5
                    vv
clus                 STAGE IV
  17Q GAIN MUTATED          1
  17Q GAIN WILD-TYPE        4
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA                3                 27
  STAGE IIB                8                113
  STAGE III                0                  5
  STAGE IV                 1                  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     1   2  12   0
  17Q GAIN WILD-TYPE   6  22 135   4
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                1                  6
  T2                2                 22
  T3               12                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"
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6   8
  17Q GAIN WILD-TYPE  44 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6    8
  17Q GAIN WILD-TYPE   44  121
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                6                 44
  1                8                121
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    5  1
  17Q GAIN WILD-TYPE 80  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    1
  17Q GAIN WILD-TYPE   80    4
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                5                 80
  1                1                  4
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    9  8
  17Q GAIN WILD-TYPE 74 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      9    8
  17Q GAIN WILD-TYPE   74   93
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                9                 74
  MALE                  8                 93
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     8   8
  17Q GAIN WILD-TYPE 114  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      8    8
  17Q GAIN WILD-TYPE  114   34
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 8                114
  YES                8                 34
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17Q GAIN MUTATED                                    10
  17Q GAIN WILD-TYPE                                 143
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17Q GAIN MUTATED                                       7
  17Q GAIN WILD-TYPE                                    18
                    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
D31V9, multiclass
                                                  clus
vv                                                 17Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 17Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             143
  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"
D31V10, continuous
D31V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    10   6   0   0
  17Q GAIN WILD-TYPE 101  47   5   4
D31V12, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               10                101
  R1                6                 47
  R2                0                  5
  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"
D31V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         1    15
  17Q GAIN WILD-TYPE    11                         6   146
D31V14, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   15                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"
D31V15, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  13
  17Q GAIN WILD-TYPE   5 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   13
  17Q GAIN WILD-TYPE    5  123
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               13                123
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   13 15
  18P GAIN WILD-TYPE 73 81
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                28                154 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                 81 
$`18P GAIN MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQE 
        2.63        42.31        14.47        15.22         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        36.26        15.95        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FZ-5921 TCGA-H8-A6C1 TCGA-HV-A5A6 TCGA-HV-A7OP TCGA-HZ-7289 
        4.04         5.10        22.06        66.94        32.15        21.73 
TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-IB-7893 TCGA-IB-8127 
       19.50        20.19        17.92         5.26         3.85        17.16 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-PZ-A5RE TCGA-US-A776 
        8.22        15.88        15.45        39.98 

$`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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        32.81        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       24.43        75.12        71.74        10.98         9.50        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 
       12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-AA8V 
       13.84         4.21         7.63         9.50         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
       17.49         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        19.59         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-HZ-A9TJ 
        6.38        21.60        10.85         1.08         0.23        19.82 
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-7897 TCGA-IB-8126 TCGA-IB-A5SO 
       15.81        19.66        21.30        15.98         2.47        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-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-Q3-A5QY 
       12.92        12.46        10.29        19.20         8.78        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        24.23        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-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              2.63               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             68.52              90.12 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             17.54              13.99 
[1] "2.6 - 68.5 (17.5)" "0.0 - 90.1 (14.0)"
[1] "hr=" "1.3"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  18P GAIN MUTATED         0        0        2         5        20         0
  18P GAIN WILD-TYPE       1        5       13        25       101         5
                    vv
clus                 STAGE IV
  18P GAIN MUTATED          1
  18P GAIN WILD-TYPE        4
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA                5                 25
  STAGE IIB               20                101
  STAGE III                0                  5
  STAGE IV                 1                  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
  18P GAIN MUTATED     0   4  24   0
  18P GAIN WILD-TYPE   7  20 123   4
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                  7
  T2                4                 20
  T3               24                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"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     7  20
  18P GAIN WILD-TYPE  43 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7   20
  18P GAIN WILD-TYPE   43  109
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                7                 43
  1               20                109
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   12  1
  18P GAIN WILD-TYPE 73  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     12    1
  18P GAIN WILD-TYPE   73    4
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               12                 73
  1                1                  4
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    9 19
  18P GAIN WILD-TYPE 74 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      9   19
  18P GAIN WILD-TYPE   74   82
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                9                 74
  MALE                 19                 82
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    19   6
  18P GAIN WILD-TYPE 103  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     19    6
  18P GAIN WILD-TYPE  103   36
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                19                103
  YES                6                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18P GAIN MUTATED                                    19
  18P GAIN WILD-TYPE                                 134
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18P GAIN MUTATED                                       7
  18P GAIN WILD-TYPE                                    18
                    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
D32V9, multiclass
                                                  clus
vv                                                 18P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 18P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             134
  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"
D32V10, continuous
D32V11, continuous
                    vv
clus                 R0 R1 R2 RX
  18P GAIN MUTATED   18  7  0  1
  18P GAIN WILD-TYPE 93 46  5  3
D32V12, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               18                 93
  R1                7                 46
  R2                0                  5
  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"
D32V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       2                         0    25
  18P GAIN WILD-TYPE     9                         7   136
D32V14, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    2                  9
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   25                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"
D32V15, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  18
  18P GAIN WILD-TYPE   5 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   18
  18P GAIN WILD-TYPE    5  118
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               18                118
[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 78 92
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                170 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 92 
$`18Q GAIN MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IV TCGA-FB-AAPP 
        2.63        15.22        45.47        68.52        36.26        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        39.98 

$`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        42.31        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        58.98        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        33.57        60.95        90.12        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       32.81        15.06        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        12.66        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       32.15        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        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-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-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        24.23        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              2.63               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             68.52              90.12 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            15.915             14.995 
[1] "2.6 - 68.5 (15.9)" "0.0 - 90.1 (15.0)"
[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        5       13        29       112         5
                    vv
clus                 STAGE IV
  18Q GAIN MUTATED          0
  18Q GAIN WILD-TYPE        5
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA                1                 29
  STAGE IIB                9                112
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   7  21 138   4
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                  7
  T2                3                 21
  T3                9                138
  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  48 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    9
  18Q GAIN WILD-TYPE   48  120
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                2                 48
  1                9                120
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  0
  18Q GAIN WILD-TYPE 81  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE   81    5
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                4                 81
  1                0                  5
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  8
  18Q GAIN WILD-TYPE 79 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    8
  18Q GAIN WILD-TYPE   79   93
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                 79
  MALE                  8                 93
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     8   3
  18Q GAIN WILD-TYPE 114  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      8    3
  18Q GAIN WILD-TYPE  114   39
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 8                114
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18Q GAIN MUTATED                                     7
  18Q GAIN WILD-TYPE                                 146
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18Q GAIN MUTATED                                       3
  18Q GAIN WILD-TYPE                                    22
                    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
D33V9, 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                             146
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            22
  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"
D33V10, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 54 
        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-HV-AA8V         TCGA-HZ-A77Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-7887         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-AAUU         TCGA-IB-AAUV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-XN-A8T5         TCGA-YY-A8LH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D33V11, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 44 
        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-XN-A8T5         TCGA-YY-A8LH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     6   5   0   0
  18Q GAIN WILD-TYPE 105  48   5   4
D33V12, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                6                105
  R1                5                 48
  R2                0                  5
  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"
D33V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0    11
  18Q GAIN WILD-TYPE    11                         7   150
D33V14, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   11                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"
D33V15, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   8
  18Q GAIN WILD-TYPE   5 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    8
  18Q GAIN WILD-TYPE    5  128
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                8                128
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   12  5
  19P GAIN WILD-TYPE 74 91
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                17                165 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 91 
$`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        32.81        36.26 
TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-HV-A5A5 TCGA-HZ-A9TJ 
        3.12        12.66        34.82        23.54         9.50        19.82 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-AAUQ TCGA-US-A776 TCGA-YB-A89D 
        4.04        17.16         6.02        39.98        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        42.31        31.86        15.91        14.47        15.22 
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        58.98        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        33.57        60.95        90.12        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        24.43        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.50        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        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
        4.21         7.63        66.94         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       17.49        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 
       19.59         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-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-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-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86        14.17        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-A8RO 
        3.12        15.32         9.40         0.30        24.23        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-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              2.63               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             68.52              90.12 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             17.16              15.12 
[1] "2.6 - 68.5 (17.2)" "0.0 - 90.1 (15.1)"
[1] "hr=" "2.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  19P GAIN MUTATED         0        0        3         1        12         0
  19P GAIN WILD-TYPE       1        5       12        29       109         5
                    vv
clus                 STAGE IV
  19P GAIN MUTATED          1
  19P GAIN WILD-TYPE        4
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 3                 12
  STAGE IIA                1                 29
  STAGE IIB               12                109
  STAGE III                0                  5
  STAGE IV                 1                  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  12   0
  19P GAIN WILD-TYPE   7  19 135   4
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                0                  7
  T2                5                 19
  T3               12                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"
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     4  12
  19P GAIN WILD-TYPE  46 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4   12
  19P GAIN WILD-TYPE   46  117
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                4                 46
  1               12                117
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    7  1
  19P GAIN WILD-TYPE 78  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7    1
  19P GAIN WILD-TYPE   78    4
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                7                 78
  1                1                  4
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    4 13
  19P GAIN WILD-TYPE 79 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4   13
  19P GAIN WILD-TYPE   79   88
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                4                 79
  MALE                 13                 88
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    12   4
  19P GAIN WILD-TYPE 110  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     12    4
  19P GAIN WILD-TYPE  110   38
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                12                110
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19P GAIN MUTATED                                    11
  19P GAIN WILD-TYPE                                 142
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19P GAIN MUTATED                                       5
  19P GAIN WILD-TYPE                                    20
                    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
D34V9, multiclass
                                                  clus
vv                                                 19P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 19P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             142
  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"
D34V10, continuous
D34V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED     7   7   0   1
  19P GAIN WILD-TYPE 104  46   5   3
D34V12, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                7                104
  R1                7                 46
  R2                0                  5
  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"
D34V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         0    16
  19P GAIN WILD-TYPE    10                         7   145
D34V14, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   16                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"
D34V15, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  12
  19P GAIN WILD-TYPE   5 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   12
  19P GAIN WILD-TYPE    5  124
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               12                124
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   17 11
  19Q GAIN WILD-TYPE 69 85
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                28                154 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                 85 
$`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        42.31         9.60        45.47 
TCGA-3A-A9IN TCGA-3A-A9IS TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPY 
       68.52        32.81        36.26         3.12        12.66        34.82 
TCGA-FB-AAPZ TCGA-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HZ-7922 
       23.54         4.21         9.50        66.94         8.28         0.13 
TCGA-HZ-8001 TCGA-HZ-A9TJ TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8127 TCGA-IB-A6UG 
       23.21        19.82         4.04        21.30        17.16         1.35 
TCGA-IB-AAUQ TCGA-LB-A7SX TCGA-US-A776 TCGA-YB-A89D 
        6.02        12.92        39.98        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        15.22        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       43.50        20.84         7.36        24.26        33.57        60.95 
TCGA-3A-A9IL TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       90.12        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 
       24.43        75.12        71.74        10.98         9.50        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        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
        0.03        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-HV-A5A4 TCGA-HV-A7OP TCGA-HV-AA8V 
       12.89        13.84        22.06         7.63        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       17.49        21.73         0.92        19.50         7.76         0.26 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       27.62        20.19        17.03        12.03        19.59         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-7893 TCGA-IB-7897 TCGA-IB-8126 
       43.79        15.81        19.66         3.85        15.98         2.47 
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-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-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        24.23 
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-XN-A8T3 
       18.67        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        12.76        66.28        15.35 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.13               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             68.52              90.12 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             15.04              15.17 
[1] "0.1 - 68.5 (15.0)" "0.0 - 90.1 (15.2)"
[1] "hr=" "1.7"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  19Q GAIN MUTATED         0        0        3         5        18         1
  19Q GAIN WILD-TYPE       1        5       12        25       103         4
                    vv
clus                 STAGE IV
  19Q GAIN MUTATED          1
  19Q GAIN WILD-TYPE        4
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 3                 12
  STAGE IIA                5                 25
  STAGE IIB               18                103
  STAGE III                1                  4
  STAGE IV                 1                  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  22   1
  19Q GAIN WILD-TYPE   7  19 125   3
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                0                  7
  T2                5                 19
  T3               22                125
  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     8  18
  19Q GAIN WILD-TYPE  42 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      8   18
  19Q GAIN WILD-TYPE   42  111
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                8                 42
  1               18                111
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   13  1
  19Q GAIN WILD-TYPE 72  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13    1
  19Q GAIN WILD-TYPE   72    4
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               13                 72
  1                1                  4
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    8 20
  19Q GAIN WILD-TYPE 75 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      8   20
  19Q GAIN WILD-TYPE   75   81
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                8                 75
  MALE                 20                 81
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    21   5
  19Q GAIN WILD-TYPE 101  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     21    5
  19Q GAIN WILD-TYPE  101   37
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                21                101
  YES                5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19Q GAIN MUTATED                                    21
  19Q GAIN WILD-TYPE                                 132
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19Q GAIN MUTATED                                       6
  19Q GAIN WILD-TYPE                                    19
                    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
D35V9, multiclass
                                                  clus
vv                                                 19Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 19Q GAIN 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"
D35V10, continuous
D35V11, continuous
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED   13 10  1  1
  19Q GAIN WILD-TYPE 98 43  4  3
D35V12, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               13                 98
  R1               10                 43
  R2                1                  4
  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"
D35V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       4                         1    23
  19Q GAIN WILD-TYPE     7                         6   138
D35V14, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    4                  7
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   23                138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0  17
  19Q GAIN WILD-TYPE   5 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   17
  19Q GAIN WILD-TYPE    5  119
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               17                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 68 81
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                33                149 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                15                 81 
$`20P GAIN MUTATED`
TCGA-2J-AABF TCGA-2J-AABP TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IO 
       22.72        15.22         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 
       32.81        36.26        24.43        12.66        16.37        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        39.98 
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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX 
       33.57        60.95        90.12        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         9.50        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 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP 
        4.21         7.63         9.50        66.94         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       30.25        17.49         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        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       19.82        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-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-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-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        24.23        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-Z5-AAPL 
       16.37        31.27        23.67        12.76        15.35 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.13               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             68.52              90.12 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             15.85              14.93 
[1] "0.1 - 68.5 (15.8)" "0.0 - 90.1 (14.9)"
[1] "hr=" "1.3"
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        4       10        26        98         5
                    vv
clus                 STAGE IV
  20P GAIN MUTATED          0
  20P GAIN WILD-TYPE        5
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  4
  STAGE IB                 5                 10
  STAGE IIA                4                 26
  STAGE IIB               23                 98
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   6  17 122   4
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                1                  6
  T2                7                 17
  T3               25                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"
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     9  23
  20P GAIN WILD-TYPE  41 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      9   23
  20P GAIN WILD-TYPE   41  106
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                9                 41
  1               23                106
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   10  0
  20P GAIN WILD-TYPE 75  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     10    0
  20P GAIN WILD-TYPE   75    5
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               10                 75
  1                0                  5
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   12 22
  20P GAIN WILD-TYPE 71 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12   22
  20P GAIN WILD-TYPE   71   79
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               12                 71
  MALE                 22                 79
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    22   9
  20P GAIN WILD-TYPE 100  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     22    9
  20P GAIN WILD-TYPE  100   33
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                22                100
  YES                9                 33
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20P GAIN MUTATED                                    24
  20P GAIN WILD-TYPE                                 129
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20P GAIN MUTATED                                       8
  20P GAIN WILD-TYPE                                    17
                    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
D36V9, 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                             129
  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"
D36V10, continuous
D36V11, continuous
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   20 10  0  2
  20P GAIN WILD-TYPE 91 43  5  2
D36V12, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               20                 91
  R1               10                 43
  R2                0                  5
  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"
D36V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         1    31
  20P GAIN WILD-TYPE    11                         6   130
D36V14, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   31                130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1  26
  20P GAIN WILD-TYPE   4 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   26
  20P GAIN WILD-TYPE    4  110
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               26                110
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   24 20
  20Q GAIN WILD-TYPE 62 76
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                44                138 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                20                 76 
$`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        15.22         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        32.81        36.26        24.43        12.66 
TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ6 TCGA-FZ-5921 
       16.37        15.95        23.54        15.55         8.02         5.10 
TCGA-FZ-5926 TCGA-HV-A5A3 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-8005 
       17.79         4.21        21.73         0.92         0.13         3.95 
TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A9TJ TCGA-IB-7646 TCGA-IB-7886 TCGA-IB-7890 
        5.26         1.08        19.82         4.77         4.04        19.66 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUU 
       17.16        15.85        21.90         8.22        15.88         8.05 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-S4-A8RO TCGA-US-A776 TCGA-US-A77E 
        9.14        12.46        19.20        17.26        39.98        14.14 
TCGA-YB-A89D TCGA-YY-A8LH 
       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 
       42.31        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 
       58.98        43.50         7.36        24.26        33.57        60.95 
TCGA-3A-A9IL TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY 
       90.12        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         9.50        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         0.03        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-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84        22.06         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7920 
        8.28        32.15        30.25        17.49        19.50         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-8636 TCGA-HZ-8638 
       19.59         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-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-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-A6UG TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       15.12        20.88         1.35         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-LB-A7SX TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
        7.56        12.92        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-A8RP 
        3.12        15.32         9.40         0.30        24.23        23.08 
TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.03        16.37        31.27        23.67        12.76        15.35 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.13               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             68.52              90.12 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            15.865             14.700 
[1] "0.1 - 68.5 (15.9)" "0.0 - 90.1 (14.7)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  20Q GAIN MUTATED         0        1        5         8        28         1
  20Q GAIN WILD-TYPE       1        4       10        22        93         4
                    vv
clus                 STAGE IV
  20Q GAIN MUTATED          1
  20Q GAIN WILD-TYPE        4
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  4
  STAGE IB                 5                 10
  STAGE IIA                8                 22
  STAGE IIB               28                 93
  STAGE III                1                  4
  STAGE IV                 1                  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  36   0
  20Q GAIN WILD-TYPE   6  17 111   4
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                1                  6
  T2                7                 17
  T3               36                111
  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    13  29
  20Q GAIN WILD-TYPE  37 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     13   29
  20Q GAIN WILD-TYPE   37  100
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               13                 37
  1               29                100
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   17  1
  20Q GAIN WILD-TYPE 68  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     17    1
  20Q GAIN WILD-TYPE   68    4
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               17                 68
  1                1                  4
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   15 30
  20Q GAIN WILD-TYPE 68 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     15   30
  20Q GAIN WILD-TYPE   68   71
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               15                 68
  MALE                 30                 71
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   30 11
  20Q GAIN WILD-TYPE 92 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     30   11
  20Q GAIN WILD-TYPE   92   31
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                30                 92
  YES               11                 31
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20Q GAIN MUTATED                                    34
  20Q GAIN WILD-TYPE                                 119
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20Q GAIN MUTATED                                       9
  20Q GAIN WILD-TYPE                                    16
                    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
D37V9, multiclass
                                                  clus
vv                                                 20Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            34
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 20Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             119
  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"
D37V10, continuous
D37V11, continuous
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED   27 12  1  2
  20Q GAIN WILD-TYPE 84 41  4  2
D37V12, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               27                 84
  R1               12                 41
  R2                1                  4
  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"
D37V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       1                         1    40
  20Q GAIN WILD-TYPE    10                         6   121
D37V14, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   40                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"
D37V15, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     1  34
  20Q GAIN WILD-TYPE   4 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1   34
  20Q GAIN WILD-TYPE    4  102
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               34                102
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    3  5
  22Q GAIN WILD-TYPE 83 91
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                174 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 91 
$`22Q GAIN MUTATED`
TCGA-2J-AABP TCGA-FB-A545 TCGA-FZ-5921 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-IB-7893 
       15.22        12.66         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        42.31        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.50        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        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       32.15        30.25        17.49        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-8636 
       12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-8127 TCGA-IB-A5SO 
       19.66        21.30        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-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        7.56         9.14        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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.13               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             15.32              90.12 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              8.88              15.40 
[1] "0.1 - 15.3 (8.9)"  "0.0 - 90.1 (15.4)"
[1] "hr=" "3.1"
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        5       15        29       114         5
                    vv
clus                 STAGE IV
  22Q GAIN MUTATED          0
  22Q GAIN WILD-TYPE        5
D38V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 0                 15
  STAGE IIA                1                 29
  STAGE IIB                7                114
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   7  24 139   4
D38V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                0                  7
  T2                0                 24
  T3                8                139
  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  49 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    7
  22Q GAIN WILD-TYPE   49  122
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                1                 49
  1                7                122
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  0
  22Q GAIN WILD-TYPE 81  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    0
  22Q GAIN WILD-TYPE   81    5
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                4                 81
  1                0                  5
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    6  2
  22Q GAIN WILD-TYPE 77 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      6    2
  22Q GAIN WILD-TYPE   77   99
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                6                 77
  MALE                  2                 99
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     5   2
  22Q GAIN WILD-TYPE 117  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5    2
  22Q GAIN WILD-TYPE  117   40
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 5                117
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  22Q GAIN MUTATED                                     6
  22Q GAIN WILD-TYPE                                 147
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  22Q GAIN MUTATED                                       1
  22Q GAIN WILD-TYPE                                    24
                    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
D38V9, 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                             147
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            24
  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"
D38V10, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 55 
        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-HV-AA8V         TCGA-HZ-A77Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7887         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-AAUU         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RM         TCGA-S4-A8RP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUL         TCGA-XN-A8T5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"22Q GAIN WILD-TYPE" 
D38V11, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 45 
        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-XN-A8T5         TCGA-YY-A8LH 
"22Q GAIN WILD-TYPE" "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 107  51   5   4
D38V12, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                4                107
  R1                2                 51
  R2                0                  5
  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"
D38V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         1     6
  22Q GAIN WILD-TYPE    11                         6   155
D38V14, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    6                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"
D38V15, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0   6
  22Q GAIN WILD-TYPE   5 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    6
  22Q GAIN WILD-TYPE    5  130
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                6                130
[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 79 95
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8               174 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                95 
$`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        36.26        23.54 
TCGA-LB-A7SX TCGA-US-A776 
       12.92        39.98 

$`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        42.31        31.86        15.91        14.47        15.22 
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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IR 
        7.36        24.26        33.57        60.95        90.12        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       32.81        15.06        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        12.66        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
        9.50        66.94         8.28        32.15        30.25        17.49 
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        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        7.56         9.14        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 
       24.23        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             2.63              0.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            68.52             90.12 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           38.120            14.995 
[1] "2.6 - 68.5 (38.1)" "0.0 - 90.1 (15.0)"
[1] "hr=" "8.5"
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        5       13        29       117         5
                   vv
clus                STAGE IV
  XP GAIN MUTATED          0
  XP GAIN WILD-TYPE        5
D39V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                2                13
  STAGE IIA               1                29
  STAGE IIB               4               117
  STAGE III               0                 5
  STAGE IV                0                 5
[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   7  21 143   4
D39V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               0                 7
  T2               3                21
  T3               4               143
  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  48 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    4
  XP GAIN WILD-TYPE   48  125
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               2                48
  1               4               125
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    1  0
  XP GAIN WILD-TYPE 84  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1    0
  XP GAIN WILD-TYPE   84    5
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0               1                84
  1               0                 5
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    3  5
  XP GAIN WILD-TYPE 80 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3    5
  XP GAIN WILD-TYPE   80   96
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               3                80
  MALE                 5                96
[1] 2 2
[1] FALSE
D39V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     6   1
  XP GAIN WILD-TYPE 116  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      6    1
  XP GAIN WILD-TYPE  116   41
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                6               116
  YES               1                41
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XP GAIN MUTATED                                     3
  XP GAIN WILD-TYPE                                 150
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XP GAIN MUTATED                                       4
  XP GAIN WILD-TYPE                                    21
                   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
D39V9, 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                            150
  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"
D39V10, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                55 
       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-HV-AA8V        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-7887        TCGA-IB-7891 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
D39V11, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                45 
       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-XN-A8T5 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-YY-A8LH 
"XP GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED     4   4   0   0
  XP GAIN WILD-TYPE 107  49   5   4
D39V12, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0               4               107
  R1               4                49
  R2               0                 5
  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"
D39V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         1     7
  XP GAIN WILD-TYPE    11                         6   154
D39V14, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   7               154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0   6
  XP GAIN WILD-TYPE   5 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0    6
  XP GAIN WILD-TYPE    5  130
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6               130
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   10  2
  XQ GAIN WILD-TYPE 76 94
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12               170 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                94 
$`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        36.26         0.03        23.54 
TCGA-HZ-8001 TCGA-HZ-A9TJ TCGA-IB-A7LX TCGA-LB-A7SX TCGA-Q3-AA2A TCGA-S4-A8RO 
       23.21        19.82         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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        15.06        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.50        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        12.66 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
        9.50        66.94         8.28        32.15        30.25        17.49 
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-8002 TCGA-HZ-8003 TCGA-HZ-8005 
       27.62        20.19        17.03        12.03        19.59         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-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-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-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-RB-A7B8 
       10.29        19.20         8.78        15.45        13.68        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40         0.30        24.23        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.03              0.13 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            68.52             90.12 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           21.515            14.995 
[1] "0.0 - 68.5 (21.5)" "0.1 - 90.1 (15.0)"
[1] "hr=" "4.9"
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        5       12        30       114         4
                   vv
clus                STAGE IV
  XQ GAIN MUTATED          1
  XQ GAIN WILD-TYPE        4
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                3                12
  STAGE IIA               0                30
  STAGE IIB               7               114
  STAGE III               1                 4
  STAGE IV                1                 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   8   1
  XQ GAIN WILD-TYPE   7  21 139   3
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               0                 7
  T2               3                21
  T3               8               139
  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     3   8
  XQ GAIN WILD-TYPE  47 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3    8
  XQ GAIN WILD-TYPE   47  121
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               3                47
  1               8               121
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    1  1
  XQ GAIN WILD-TYPE 84  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    1
  XQ GAIN WILD-TYPE   84    4
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               1                84
  1               1                 4
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    7  6
  XQ GAIN WILD-TYPE 76 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7    6
  XQ GAIN WILD-TYPE   76   95
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               7                76
  MALE                 6                95
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     9   2
  XQ GAIN WILD-TYPE 113  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      9    2
  XQ GAIN WILD-TYPE  113   40
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                9               113
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XQ GAIN MUTATED                                     8
  XQ GAIN WILD-TYPE                                 145
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XQ GAIN MUTATED                                       5
  XQ GAIN WILD-TYPE                                    20
                   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
D40V9, multiclass
                                                  clus
vv                                                 XQ GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 XQ GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            145
  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"
D40V10, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                54 
       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-HV-AA8V        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-7887        TCGA-IB-7891        TCGA-IB-8126 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D40V11, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                44 
       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-XN-A8T5        TCGA-YY-A8LH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED     8   4   0   1
  XQ GAIN WILD-TYPE 103  49   5   3
D40V12, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               8               103
  R1               4                49
  R2               0                 5
  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"
D40V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         1    12
  XQ GAIN WILD-TYPE    11                         6   149
D40V14, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  12               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"
D40V15, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  11
  XQ GAIN WILD-TYPE   4 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   11
  XQ GAIN WILD-TYPE    4  125
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              11               125
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   15 21
  1P LOSS WILD-TYPE 71 75
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36               146 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21                75 
$`1P LOSS MUTATED`
TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABO TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       42.31        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        90.12        32.81        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-HV-A5A5 TCGA-HV-A7OP TCGA-HZ-8005 TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7886 
        9.50        32.15         3.95         5.26         0.23         4.04 
TCGA-IB-7889 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A7LX TCGA-IB-A7M4 
       15.81        17.16        15.85        15.12         8.22        15.88 
TCGA-IB-AAUN TCGA-LB-A8F3 TCGA-OE-A75W TCGA-S4-A8RM TCGA-S4-A8RO TCGA-YY-A8LH 
        4.73        12.46         8.78        24.23        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        15.22        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN 
       20.84         7.36        24.26        33.57        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        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       24.43        75.12        10.98         9.50        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 
       66.94         8.28        30.25        17.49        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        19.59         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-A9TJ TCGA-IB-7644 
        6.38        21.60        10.85         1.08        19.82        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-7890 TCGA-IB-7891 
       15.65        41.33         3.62        43.79        19.66        21.30 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST 
        3.85        15.98         2.47        12.00         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       21.90         1.35         0.26         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-PZ-A5RE TCGA-Q3-A5QY 
        9.14        12.92        10.29        19.20        15.45        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-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       39.98        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.23              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            90.12             75.12 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           15.335            15.140 
[1] "0.2 - 90.1 (15.3)" "0.0 - 75.1 (15.1)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  1P LOSS MUTATED         1        1        3         9        21         1
  1P LOSS WILD-TYPE       0        4       12        21       100         4
                   vv
clus                STAGE IV
  1P LOSS MUTATED          0
  1P LOSS WILD-TYPE        5
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                1                 4
  STAGE IB                3                12
  STAGE IIA               9                21
  STAGE IIB              21               100
  STAGE III               1                 4
  STAGE IV                0                 5
[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  29   1
  1P LOSS WILD-TYPE   5  20 118   3
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               2                 5
  T2               4                20
  T3              29               118
  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  22
  1P LOSS WILD-TYPE  38 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     12   22
  1P LOSS WILD-TYPE   38  107
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              12                38
  1              22               107
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   16  0
  1P LOSS WILD-TYPE 69  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     16    0
  1P LOSS WILD-TYPE   69    5
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              16                69
  1               0                 5
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   12 24
  1P LOSS WILD-TYPE 71 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     12   24
  1P LOSS WILD-TYPE   71   77
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              12                71
  MALE                24                77
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   26  8
  1P LOSS WILD-TYPE 96 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     26    8
  1P LOSS WILD-TYPE   96   34
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               26                96
  YES               8                34
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1P LOSS MUTATED                                    30
  1P LOSS WILD-TYPE                                 123
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1P LOSS MUTATED                                       5
  1P LOSS WILD-TYPE                                    20
                   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
D41V9, multiclass
                                                  clus
vv                                                 1P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           30
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 1P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            123
  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"
D41V10, continuous
D41V11, continuous
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   25  9  0  0
  1P LOSS WILD-TYPE 86 44  5  4
D41V12, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              25                86
  R1               9                44
  R2               0                 5
  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"
D41V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       3                         2    31
  1P LOSS WILD-TYPE     8                         5   130
D41V14, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   3                 8
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  31               130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1  25
  1P LOSS WILD-TYPE   4 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   25
  1P LOSS WILD-TYPE    4  111
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              25               111
[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 82 92
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8               174 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                92 
$`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        90.12        32.81         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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQI 
       15.22        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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        24.26        33.57        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        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.50        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP 
        4.21         7.63         9.50        66.94         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-7890 
       15.65        41.33         4.04         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-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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             3.95              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            90.12             75.12 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           15.865            14.995 
[1] "4.0 - 90.1 (15.9)" "0.0 - 75.1 (15.0)"
[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        5       14        29       116         5
                   vv
clus                STAGE IV
  1Q LOSS MUTATED          0
  1Q LOSS WILD-TYPE        5
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               1                29
  STAGE IIB               5               116
  STAGE III               0                 5
  STAGE IV                0                 5
[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   6  23 141   4
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               1                 6
  T2               1                23
  T3               6               141
  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  48 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    5
  1Q LOSS WILD-TYPE   48  124
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               2                48
  1               5               124
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  0
  1Q LOSS WILD-TYPE 82  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE   82    5
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               3                82
  1               0                 5
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    2  6
  1Q LOSS WILD-TYPE 81 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    6
  1Q LOSS WILD-TYPE   81   95
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               2                81
  MALE                 6                95
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     8   0
  1Q LOSS WILD-TYPE 114  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8    0
  1Q LOSS WILD-TYPE  114   42
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                8               114
  YES               0                42
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1Q LOSS MUTATED                                     6
  1Q LOSS WILD-TYPE                                 147
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1Q LOSS MUTATED                                       2
  1Q LOSS WILD-TYPE                                    23
                   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
D42V9, 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                            147
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           23
  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"
D42V10, continuous
D42V11, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                45 
       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-XN-A8T5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-YY-A8LH 
"1Q LOSS WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     5   3   0   0
  1Q LOSS WILD-TYPE 106  50   5   4
D42V12, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               5               106
  R1               3                50
  R2               0                 5
  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"
D42V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0     8
  1Q LOSS WILD-TYPE    11                         7   153
D42V14, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   8               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"
D42V15, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   5
  1Q LOSS WILD-TYPE   5 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    5
  1Q LOSS WILD-TYPE    5  131
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5               131
[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 80 91
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               171 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5                91 
$`2P LOSS MUTATED`
TCGA-2J-AABP TCGA-3A-A9I9 TCGA-3A-A9IL TCGA-3A-A9IS TCGA-H6-8124 TCGA-HZ-7289 
       15.22        20.84        90.12        32.81        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        39.98 

$`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        42.31        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        58.98        43.50 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        24.26        33.57        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        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       75.12        71.74        10.98         9.50        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       16.37         0.03        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-HV-A5A3 
       20.35        15.78        17.79        13.84        22.06         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
        7.63         9.50        66.94         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       17.49         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        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
        1.08         0.23        19.82        12.95        49.38        21.90 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
       15.35        19.82        15.65        41.33         4.04         3.62 
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        24.23        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             4.77              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            90.12             75.12 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            21.73             14.93 
[1] "4.8 - 90.1 (21.7)" "0.0 - 75.1 (14.9)"
[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        5       14        27       115         5
                   vv
clus                STAGE IV
  2P LOSS MUTATED          0
  2P LOSS WILD-TYPE        5
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               3                27
  STAGE IIB               6               115
  STAGE III               0                 5
  STAGE IV                0                 5
[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   6  23 138   4
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               1                 6
  T2               1                23
  T3               9               138
  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  46 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    6
  2P LOSS WILD-TYPE   46  123
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               4                46
  1               6               123
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    5  0
  2P LOSS WILD-TYPE 80  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    0
  2P LOSS WILD-TYPE   80    5
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               5                80
  1               0                 5
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    5  6
  2P LOSS WILD-TYPE 78 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    6
  2P LOSS WILD-TYPE   78   95
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               5                78
  MALE                 6                95
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     8   3
  2P LOSS WILD-TYPE 114  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8    3
  2P LOSS WILD-TYPE  114   39
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                8               114
  YES               3                39
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2P LOSS MUTATED                                     6
  2P LOSS WILD-TYPE                                 147
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2P LOSS MUTATED                                       3
  2P LOSS WILD-TYPE                                    22
                   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
D43V9, 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                            147
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           22
  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"
D43V10, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                54 
       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-HV-AA8V 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-IB-7644 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-7886 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-7887        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-AAUU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V11, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                45 
       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-XN-A8T5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-YY-A8LH 
"2P LOSS WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     7   3   0   1
  2P LOSS WILD-TYPE 104  50   5   3
D43V12, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               7               104
  R1               3                50
  R2               0                 5
  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"
D43V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       1                         1     9
  2P LOSS WILD-TYPE    10                         6   152
D43V14, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   9               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"
D43V15, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  10
  2P LOSS WILD-TYPE   5 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   10
  2P LOSS WILD-TYPE    5  126
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              10               126
[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 82 95
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               177 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                95 
$`2Q LOSS MUTATED`
TCGA-3A-A9IL TCGA-3A-A9IS TCGA-H6-8124 TCGA-IB-7646 TCGA-US-A776 
       90.12        32.81        12.89         4.77        39.98 

$`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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       43.50        20.84         7.36        24.26        33.57        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        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       32.15        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
       19.82        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-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        24.23        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             4.77              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            90.12             75.12 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            32.81             15.12 
[1] "4.8 - 90.1 (32.8)" "0.0 - 75.1 (15.1)"
[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        5       14        29       119         5
                   vv
clus                STAGE IV
  2Q LOSS MUTATED          0
  2Q LOSS WILD-TYPE        5
D44V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               1                29
  STAGE IIB               2               119
  STAGE III               0                 5
  STAGE IV                0                 5
[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   6  23 144   4
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               1                 6
  T2               1                23
  T3               3               144
  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  48 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    2
  2Q LOSS WILD-TYPE   48  127
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               2                48
  1               2               127
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    2  0
  2Q LOSS WILD-TYPE 83  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    0
  2Q LOSS WILD-TYPE   83    5
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               2                83
  1               0                 5
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    2  3
  2Q LOSS WILD-TYPE 81 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    3
  2Q LOSS WILD-TYPE   81   98
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               2                81
  MALE                 3                98
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     4   1
  2Q LOSS WILD-TYPE 118  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    1
  2Q LOSS WILD-TYPE  118   41
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                4               118
  YES               1                41
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2Q LOSS MUTATED                                     2
  2Q LOSS WILD-TYPE                                 151
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2Q LOSS MUTATED                                       2
  2Q LOSS WILD-TYPE                                    23
                   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
D44V9, 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                            151
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           23
  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"
D44V10, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                55 
       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-HV-AA8V        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-7887        TCGA-IB-7891        TCGA-IB-8126 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A7SX        TCGA-LB-A9Q5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP        TCGA-US-A774 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D44V11, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                45 
       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-XN-A8T5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-YY-A8LH 
"2Q LOSS WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     4   1   0   0
  2Q LOSS WILD-TYPE 107  52   5   4
D44V12, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               4               107
  R1               1                52
  R2               0                 5
  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"
D44V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0     5
  2Q LOSS WILD-TYPE    11                         7   156
D44V14, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   5               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   5
  2Q LOSS WILD-TYPE   5 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    5
  2Q LOSS WILD-TYPE    5  131
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5               131
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   16 20
  3P LOSS WILD-TYPE 70 76
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               36               146 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               20                76 
$`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        15.22         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        58.98        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-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8005 TCGA-HZ-A4BK TCGA-HZ-A77O 
       17.49         0.92        20.19         3.95        21.60         5.26 
TCGA-HZ-A8P1 TCGA-IB-7647 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-8127 TCGA-IB-A5SP 
        0.23        21.90         4.04         3.62        17.16        15.85 
TCGA-IB-A7LX TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-RB-AA9M TCGA-YY-A8LH 
        8.22         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        42.31        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        43.50        20.84         7.36 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IR TCGA-3A-A9IS 
       33.57        60.95        90.12        68.52        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        12.66        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7289 
        9.50        66.94         8.28        32.15        30.25        21.73 
TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
       19.50         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        19.59         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-A77P TCGA-HZ-A77Q TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08        19.82        12.95        49.38         4.77 
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-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-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-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-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         0.30        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       39.98        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.23              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            66.28             90.12 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           14.845            15.220 
[1] "0.2 - 66.3 (14.8)" "0.0 - 90.1 (15.2)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  3P LOSS MUTATED         0        1        1         5        26         1
  3P LOSS WILD-TYPE       1        4       14        25        95         4
                   vv
clus                STAGE IV
  3P LOSS MUTATED          0
  3P LOSS WILD-TYPE        5
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 4
  STAGE IB                1                14
  STAGE IIA               5                25
  STAGE IIB              26                95
  STAGE III               1                 4
  STAGE IV                0                 5
[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     2   4  27   1
  3P LOSS WILD-TYPE   5  20 120   3
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               2                 5
  T2               4                20
  T3              27               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"
D45V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     8  27
  3P LOSS WILD-TYPE  42 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      8   27
  3P LOSS WILD-TYPE   42  102
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               8                42
  1              27               102
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   13  0
  3P LOSS WILD-TYPE 72  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     13    0
  3P LOSS WILD-TYPE   72    5
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              13                72
  1               0                 5
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   10 26
  3P LOSS WILD-TYPE 73 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10   26
  3P LOSS WILD-TYPE   73   75
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              10                73
  MALE                26                75
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   23 11
  3P LOSS WILD-TYPE 99 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     23   11
  3P LOSS WILD-TYPE   99   31
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               23                99
  YES              11                31
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3P LOSS MUTATED                                    31
  3P LOSS WILD-TYPE                                 122
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3P LOSS MUTATED                                       4
  3P LOSS WILD-TYPE                                    21
                   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
D45V9, multiclass
                                                  clus
vv                                                 3P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           31
  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                            122
  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"
D45V10, continuous
D45V11, continuous
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED   22 12  1  1
  3P LOSS WILD-TYPE 89 41  4  3
D45V12, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              22                89
  R1              12                41
  R2               1                 4
  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"
D45V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         2    33
  3P LOSS WILD-TYPE    10                         5   128
D45V14, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  33               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0  26
  3P LOSS WILD-TYPE   5 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   26
  3P LOSS WILD-TYPE    5  110
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              26               110
[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 75 88
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19               163 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8                88 
$`3Q LOSS MUTATED`
TCGA-2J-AABP TCGA-2L-AAQI TCGA-2L-AAQM TCGA-3A-A9IO TCGA-3A-A9IS TCGA-F2-A44H 
       15.22         3.39        45.47        63.85        32.81        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        42.31        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        58.98        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IR 
       24.26        33.57        60.95        90.12        68.52        50.70 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        12.66        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       32.15        30.25        17.49        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        19.59         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-A77P TCGA-HZ-A77Q TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       21.60        10.85         1.08        19.82        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-A5SQ TCGA-IB-A5SS 
        3.85        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-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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.23              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            66.28             90.12 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            15.85             15.06 
[1] "0.2 - 66.3 (15.8)" "0.0 - 90.1 (15.1)"
[1] "hr=" "1.3"
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        5       13        27       108         5
                   vv
clus                STAGE IV
  3Q LOSS MUTATED          0
  3Q LOSS WILD-TYPE        5
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                2                13
  STAGE IIA               3                27
  STAGE IIB              13               108
  STAGE III               0                 5
  STAGE IV                0                 5
[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   7  20 133   4
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                 7
  T2               4                20
  T3              14               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"
D46V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  13
  3Q LOSS WILD-TYPE  45 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   13
  3Q LOSS WILD-TYPE   45  116
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               5                45
  1              13               116
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    7  0
  3Q LOSS WILD-TYPE 78  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      7    0
  3Q LOSS WILD-TYPE   78    5
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               7                78
  1               0                 5
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    5 14
  3Q LOSS WILD-TYPE 78 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   14
  3Q LOSS WILD-TYPE   78   87
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               5                78
  MALE                14                87
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    13   5
  3Q LOSS WILD-TYPE 109  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     13    5
  3Q LOSS WILD-TYPE  109   37
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               13               109
  YES               5                37
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3Q LOSS MUTATED                                    15
  3Q LOSS WILD-TYPE                                 138
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3Q LOSS MUTATED                                       3
  3Q LOSS WILD-TYPE                                    22
                   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
D46V9, 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                            138
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           22
  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"
D46V10, continuous
D46V11, continuous
                   vv
clus                R0 R1 R2 RX
  3Q LOSS MUTATED   13  6  0  0
  3Q LOSS WILD-TYPE 98 47  5  4
D46V12, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              13                98
  R1               6                47
  R2               0                 5
  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"
D46V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         3    16
  3Q LOSS WILD-TYPE    11                         4   145
D46V14, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  16               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"
D46V15, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  15
  3Q LOSS WILD-TYPE   5 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   15
  3Q LOSS WILD-TYPE    5  121
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              15               121
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    9 16
  4P LOSS WILD-TYPE 77 80
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               25               157 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               16                80 
$`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        58.98         7.36        24.26 
TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPZ TCGA-FB-AAQ1 
       24.43        71.74        16.37        11.61        23.54         4.04 
TCGA-FB-AAQ2 TCGA-FZ-5920 TCGA-HV-A5A6 TCGA-HV-A7OP TCGA-HZ-7918 TCGA-HZ-7925 
        5.03         2.01        66.94        32.15         0.92        20.19 
TCGA-HZ-A49I TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-A5SP TCGA-IB-A7M4 TCGA-IB-AAUO 
       10.13         4.04         3.62        15.85        15.88         7.86 
TCGA-IB-AAUQ 
        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        42.31        31.86        15.91        15.22        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        43.50        20.84        33.57        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       90.12        68.52        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 
       36.26        34.09        10.13        75.12        10.98         9.50 
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        12.66         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL 
       13.84        22.06         4.21         7.63         9.50         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       30.25        17.49        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        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        1.08         0.23        19.82        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-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-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP 
       21.90         1.35         8.22         0.26         4.73        14.17 
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 
       24.23        17.26        23.08        22.85        39.98        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.92              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            71.74             90.12 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            14.47             15.22 
[1] "0.9 - 71.7 (14.5)" "0.0 - 90.1 (15.2)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  4P LOSS MUTATED         0        0        1         3        20         0
  4P LOSS WILD-TYPE       1        5       14        27       101         5
                   vv
clus                STAGE IV
  4P LOSS MUTATED          0
  4P LOSS WILD-TYPE        5
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               3                27
  STAGE IIB              20               101
  STAGE III               0                 5
  STAGE IV                0                 5
[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     0   2  22   0
  4P LOSS WILD-TYPE   7  22 125   4
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               0                 7
  T2               2                22
  T3              22               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"
D47V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     4  20
  4P LOSS WILD-TYPE  46 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4   20
  4P LOSS WILD-TYPE   46  109
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               4                46
  1              20               109
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   14  0
  4P LOSS WILD-TYPE 71  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     14    0
  4P LOSS WILD-TYPE   71    5
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              14                71
  1               0                 5
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    6 19
  4P LOSS WILD-TYPE 77 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6   19
  4P LOSS WILD-TYPE   77   82
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               6                77
  MALE                19                82
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    17   5
  4P LOSS WILD-TYPE 105  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     17    5
  4P LOSS WILD-TYPE  105   37
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               17               105
  YES               5                37
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4P LOSS MUTATED                                    23
  4P LOSS WILD-TYPE                                 130
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4P LOSS MUTATED                                       1
  4P LOSS WILD-TYPE                                    24
                   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
D47V9, multiclass
                                                  clus
vv                                                 4P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 4P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            130
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           24
  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"
D47V10, continuous
D47V11, continuous
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED   15  9  0  0
  4P LOSS WILD-TYPE 96 44  5  4
D47V12, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              15                96
  R1               9                44
  R2               0                 5
  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"
D47V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       3                         1    21
  4P LOSS WILD-TYPE     8                         6   140
D47V14, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   3                 8
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  21               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"
D47V15, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  18
  4P LOSS WILD-TYPE   4 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   18
  4P LOSS WILD-TYPE    4  118
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              18               118
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    9 15
  4Q LOSS WILD-TYPE 77 81
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               24               158 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               15                81 
$`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        58.98        24.43        71.74        16.37 
TCGA-FB-A7DR TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5920 TCGA-HV-A5A6 
       11.61        23.54         4.04         5.03         2.01        66.94 
TCGA-HV-A7OP TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-IB-7886 TCGA-IB-A5SP 
       32.15        20.19        10.13         6.38         4.04        15.85 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-RB-AA9M TCGA-XD-AAUI 
        8.22        15.88         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        42.31        31.86        15.91        15.22 
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        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        33.57        60.95        90.12        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        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         9.50        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        12.66         0.03 
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-HV-A5A3 
       15.78        17.79        12.89        13.84        22.06         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 
        7.63         9.50         8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-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-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        0.26         4.73        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-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         0.30        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       39.98        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2.01              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            71.74             90.12 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            13.25             15.27 
[1] "2.0 - 71.7 (13.2)" "0.0 - 90.1 (15.3)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  4Q LOSS MUTATED         0        0        1         3        20         0
  4Q LOSS WILD-TYPE       1        5       14        27       101         5
                   vv
clus                STAGE IV
  4Q LOSS MUTATED          0
  4Q LOSS WILD-TYPE        5
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               3                27
  STAGE IIB              20               101
  STAGE III               0                 5
  STAGE IV                0                 5
[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     1   2  21   0
  4Q LOSS WILD-TYPE   6  22 126   4
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               1                 6
  T2               2                22
  T3              21               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"
D48V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4  20
  4Q LOSS WILD-TYPE  46 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4   20
  4Q LOSS WILD-TYPE   46  109
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               4                46
  1              20               109
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   11  0
  4Q LOSS WILD-TYPE 74  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     11    0
  4Q LOSS WILD-TYPE   74    5
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              11                74
  1               0                 5
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    5 20
  4Q LOSS WILD-TYPE 78 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5   20
  4Q LOSS WILD-TYPE   78   81
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               5                78
  MALE                20                81
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    17   5
  4Q LOSS WILD-TYPE 105  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     17    5
  4Q LOSS WILD-TYPE  105   37
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               17               105
  YES               5                37
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4Q LOSS MUTATED                                    23
  4Q LOSS WILD-TYPE                                 130
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4Q LOSS MUTATED                                       1
  4Q LOSS WILD-TYPE                                    24
                   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
D48V9, multiclass
                                                  clus
vv                                                 4Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 4Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            130
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           24
  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"
D48V10, continuous
D48V11, continuous
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   15  9  0  0
  4Q LOSS WILD-TYPE 96 44  5  4
D48V12, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              15                96
  R1               9                44
  R2               0                 5
  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"
D48V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       3                         1    21
  4Q LOSS WILD-TYPE     8                         6   140
D48V14, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   3                 8
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  21               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"
D48V15, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2  17
  4Q LOSS WILD-TYPE   3 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   17
  4Q LOSS WILD-TYPE    3  119
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              17               119
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    6  3
  5P LOSS WILD-TYPE 80 93
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9               173 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                93 
$`5P LOSS MUTATED`
TCGA-2J-AABO TCGA-2L-AAQI TCGA-FB-A545 TCGA-HV-A7OP TCGA-IB-8127 TCGA-IB-A7M4 
       14.47         3.39        12.66        32.15        17.16        15.88 
TCGA-US-A779 TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80        12.03        31.27 

$`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        42.31        31.86        15.91        15.22 
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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        33.57        60.95        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22         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        24.23        17.26        23.08        22.85        39.98 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL 
       14.14         0.39        18.67        13.81        12.99        16.37 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.39              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            32.15             90.12 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            15.88             15.12 
[1] "3.4 - 32.1 (15.9)" "0.0 - 90.1 (15.1)"
[1] "hr=" "1.6"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  5P LOSS MUTATED         0        0        1         0         8         0
  5P LOSS WILD-TYPE       1        5       14        30       113         5
                   vv
clus                STAGE IV
  5P LOSS MUTATED          0
  5P LOSS WILD-TYPE        5
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               0                30
  STAGE IIB               8               113
  STAGE III               0                 5
  STAGE IV                0                 5
[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   1   8   0
  5P LOSS WILD-TYPE   7  23 139   4
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0                 7
  T2               1                23
  T3               8               139
  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     1   8
  5P LOSS WILD-TYPE  49 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    8
  5P LOSS WILD-TYPE   49  121
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               1                49
  1               8               121
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    5  0
  5P LOSS WILD-TYPE 80  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    0
  5P LOSS WILD-TYPE   80    5
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               5                80
  1               0                 5
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    3  6
  5P LOSS WILD-TYPE 80 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3    6
  5P LOSS WILD-TYPE   80   95
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               3                80
  MALE                 6                95
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4   4
  5P LOSS WILD-TYPE 118  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    4
  5P LOSS WILD-TYPE  118   38
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                4               118
  YES               4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5P LOSS MUTATED                                     8
  5P LOSS WILD-TYPE                                 145
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5P LOSS MUTATED                                       1
  5P LOSS WILD-TYPE                                    24
                   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
D49V9, multiclass
                                                  clus
vv                                                 5P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 5P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            145
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           24
  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"
D49V10, continuous
D49V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED     4   4   0   0
  5P LOSS WILD-TYPE 107  49   5   4
D49V12, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               4               107
  R1               4                49
  R2               0                 5
  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"
D49V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       1                         0     8
  5P LOSS WILD-TYPE    10                         7   153
D49V14, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   8               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"
D49V15, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1   5
  5P LOSS WILD-TYPE   4 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    5
  5P LOSS WILD-TYPE    4  131
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               5               131
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    7  6
  5Q LOSS WILD-TYPE 79 90
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               13               169 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                90 
$`5Q LOSS MUTATED`
TCGA-2J-AABO TCGA-2J-AABP TCGA-FB-A545 TCGA-HV-A5A6 TCGA-HV-A7OP TCGA-HZ-7289 
       14.47        15.22        12.66        66.94        32.15        21.73 
TCGA-HZ-8005 TCGA-IB-8127 TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-US-A779 TCGA-XD-AAUI 
        3.95        17.16         1.35        15.88        16.80        12.03 
TCGA-XN-A8T3 
       31.27 

$`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        42.31        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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        33.57        60.95        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-AA8V 
       22.06         4.21         7.63         9.50         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       17.49         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        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        1.08         0.23        19.82        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-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-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
       15.12        20.88        21.90         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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       22.85        39.98        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        16.37        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1.35              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            66.94             90.12 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            15.88             15.06 
[1] "1.4 - 66.9 (15.9)" "0.0 - 90.1 (15.1)"
[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        1         0        12         0
  5Q LOSS WILD-TYPE       1        5       14        30       109         5
                   vv
clus                STAGE IV
  5Q LOSS MUTATED          0
  5Q LOSS WILD-TYPE        5
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               0                30
  STAGE IIB              12               109
  STAGE III               0                 5
  STAGE IV                0                 5
[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   1  12   0
  5Q LOSS WILD-TYPE   7  23 135   4
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0                 7
  T2               1                23
  T3              12               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"
D50V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1  12
  5Q LOSS WILD-TYPE  49 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   12
  5Q LOSS WILD-TYPE   49  117
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               1                49
  1              12               117
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    8  0
  5Q LOSS WILD-TYPE 77  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8    0
  5Q LOSS WILD-TYPE   77    5
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               8                77
  1               0                 5
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    5  8
  5Q LOSS WILD-TYPE 78 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    8
  5Q LOSS WILD-TYPE   78   93
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               5                78
  MALE                 8                93
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     8   4
  5Q LOSS WILD-TYPE 114  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8    4
  5Q LOSS WILD-TYPE  114   38
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                8               114
  YES               4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5Q LOSS MUTATED                                    10
  5Q LOSS WILD-TYPE                                 143
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5Q LOSS MUTATED                                       2
  5Q LOSS WILD-TYPE                                    23
                   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
D50V9, multiclass
                                                  clus
vv                                                 5Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 5Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            143
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           23
  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"
D50V10, continuous
D50V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED     6   5   0   1
  5Q LOSS WILD-TYPE 105  48   5   3
D50V12, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               6               105
  R1               5                48
  R2               0                 5
  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"
D50V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       2                         0    11
  5Q LOSS WILD-TYPE     9                         7   150
D50V14, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   2                 9
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  11               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"
D50V15, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1   8
  5Q LOSS WILD-TYPE   4 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    8
  5Q LOSS WILD-TYPE    4  128
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               8               128
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   24 40
  6P LOSS WILD-TYPE 62 56
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               64               118 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               40                56 
$`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        15.22         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 
       33.57        90.12        32.81        71.74        10.98        19.27 
TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       12.66        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-HV-A5A3 
       24.36         2.01         5.10        15.78        12.89         4.21 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7925 
        8.28        30.25        17.49        21.73        19.50        20.19 
TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       23.21         9.83        21.60         5.26        10.85         1.08 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7893 
        4.77        21.90         4.04        15.81        19.66         3.85 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       17.16        15.85        15.12        21.90         1.35         8.22 
TCGA-IB-AAUO TCGA-LB-A7SX TCGA-OE-A75W TCGA-PZ-A5RE TCGA-US-A779 TCGA-US-A77G 
        7.86        12.92         8.78        15.45        16.80         0.39 
TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       31.27        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 
       42.31        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        58.98        43.50        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        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       24.43        75.12         9.50        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        16.37         0.03        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-HV-A5A4 
       36.20        20.35        17.79        13.84        22.06         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OP TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7922 
        9.50        66.94        32.15         0.92         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
        0.26        27.62        17.03        12.03        19.59         3.95 
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-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.13         6.38         0.23        19.82        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-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-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ 
       20.88        15.88         0.26         4.73        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-M8-A5N4 TCGA-Q3-A5QY TCGA-Q3-AA2A 
        9.14        12.46        10.29        19.20        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        39.98        14.14        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-Z5-AAPL 
       12.03        16.37        23.67        15.35 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.39              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            90.12             75.12 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           15.335            14.995 
[1] "0.4 - 90.1 (15.3)" "0.0 - 75.1 (15.0)"
[1] "hr=" "1.4"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  6P LOSS MUTATED         1        1        3        11        46         2
  6P LOSS WILD-TYPE       0        4       12        19        75         3
                   vv
clus                STAGE IV
  6P LOSS MUTATED          0
  6P LOSS WILD-TYPE        5
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                1                 4
  STAGE IB                3                12
  STAGE IIA              11                19
  STAGE IIB              46                75
  STAGE III               2                 3
  STAGE IV                0                 5
[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  7 54  1
  6P LOSS WILD-TYPE  5 17 93  3
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                 5
  T2               7                17
  T3              54                93
  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   14 48
  6P LOSS WILD-TYPE 36 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14   48
  6P LOSS WILD-TYPE   36   81
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              14                36
  1              48                81
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   29  0
  6P LOSS WILD-TYPE 56  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     29    0
  6P LOSS WILD-TYPE   56    5
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              29                56
  1               0                 5
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   24 40
  6P LOSS WILD-TYPE 59 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     24   40
  6P LOSS WILD-TYPE   59   61
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              24                59
  MALE                40                61
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   43 16
  6P LOSS WILD-TYPE 79 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     43   16
  6P LOSS WILD-TYPE   79   26
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               43                79
  YES              16                26
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6P LOSS MUTATED                                    51
  6P LOSS WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6P LOSS MUTATED                                      11
  6P LOSS WILD-TYPE                                    14
                   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
D51V9, multiclass
                                                  clus
vv                                                 6P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           51
  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                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           14
  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"
D51V10, continuous
D51V11, continuous
                   vv
clus                R0 R1 R2 RX
  6P LOSS MUTATED   35 18  3  1
  6P LOSS WILD-TYPE 76 35  2  3
D51V12, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              35                76
  R1              18                35
  R2               3                 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"
D51V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       4                         2    56
  6P LOSS WILD-TYPE     7                         5   105
D51V14, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   4                 7
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  56               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    2 44
  6P LOSS WILD-TYPE  3 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   44
  6P LOSS WILD-TYPE    3   92
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              44                92
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   31 52
  6Q LOSS WILD-TYPE 55 44
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               83                99 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               52                44 
$`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        42.31        31.86        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQM 
       15.22         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        33.57        90.12        32.81 
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        12.66 
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-HV-A5A3 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       15.78        12.89         4.21         8.28        30.25        17.49 
TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8315 
       21.73        19.50         0.13        20.19        23.21         9.83 
TCGA-HZ-8636 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7646 
       17.92         5.26        10.85         1.08        12.95         4.77 
TCGA-IB-7647 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 
       21.90        41.33         4.04         3.62        15.81        19.66 
TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A6UG 
        3.85        17.16        15.85        15.12        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUU TCGA-LB-A7SX TCGA-M8-A5N4 
        8.22         4.73         7.86         8.05        12.92        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 
        8.78        15.45        24.23        23.08        39.98        16.80 
TCGA-US-A77G TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
        0.39        31.27        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IV 
       43.50        60.95        68.52        63.85        50.70        36.26 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       34.09        24.43        75.12         9.50        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        16.37         0.03 
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-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OP 
       13.84        22.06         7.63         9.50        66.94        32.15 
TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8002 
        0.92         7.76         0.26        27.62        17.03        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
       19.59         3.95        12.43        14.93         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       16.14        10.13         6.38        21.60         0.23        19.82 
TCGA-IB-7645 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7888 
       49.38        15.35        19.82        23.80        15.65        43.79 
TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST 
       21.30        15.98         2.47        12.00         7.20        20.88 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
       15.88         0.26        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-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RO 
       13.68         3.12        15.32         9.40         0.30        17.26 
TCGA-US-A774 TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       22.85        14.14        18.67        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-Z5-AAPL 
       16.37        23.67        15.35 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.13              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            90.12             75.12 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            15.45             14.40 
[1] "0.1 - 90.1 (15.4)" "0.0 - 75.1 (14.4)"
[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        4        17        55         2
  6Q LOSS WILD-TYPE       0        3       11        13        66         3
                   vv
clus                STAGE IV
  6Q LOSS MUTATED          2
  6Q LOSS WILD-TYPE        3
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                2                 3
  STAGE IB                4                11
  STAGE IIA              17                13
  STAGE IIB              55                66
  STAGE III               2                 3
  STAGE IV                2                 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
  6Q LOSS MUTATED    3  8 71  1
  6Q LOSS WILD-TYPE  4 16 76  3
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               3                 4
  T2               8                16
  T3              71                76
  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   23 58
  6Q LOSS WILD-TYPE 27 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     23   58
  6Q LOSS WILD-TYPE   27   71
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              23                27
  1              58                71
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   37  2
  6Q LOSS WILD-TYPE 48  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     37    2
  6Q LOSS WILD-TYPE   48    3
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              37                48
  1               2                 3
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   33 50
  6Q LOSS WILD-TYPE 50 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     33   50
  6Q LOSS WILD-TYPE   50   51
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              33                50
  MALE                50                51
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   57 19
  6Q LOSS WILD-TYPE 65 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     57   19
  6Q LOSS WILD-TYPE   65   23
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               57                65
  YES              19                23
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6Q LOSS MUTATED                                    70
  6Q LOSS WILD-TYPE                                  83
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6Q LOSS MUTATED                                      10
  6Q LOSS WILD-TYPE                                    15
                   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
D52V9, multiclass
                                                  clus
vv                                                 6Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           70
  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                             83
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           15
  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"
D52V10, continuous
D52V11, continuous
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED   48 24  3  1
  6Q LOSS WILD-TYPE 63 29  2  3
D52V12, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              48                63
  R1              24                29
  R2               3                 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"
D52V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       4                         2    74
  6Q LOSS WILD-TYPE     7                         5    87
D52V14, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   4                 7
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  74                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    3 58
  6Q LOSS WILD-TYPE  2 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   58
  6Q LOSS WILD-TYPE    2   78
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              58                78
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    2  1
  7P LOSS WILD-TYPE 84 95
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               179 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                95 
$`7P LOSS MUTATED`
TCGA-HZ-7922 TCGA-PZ-A5RE TCGA-XN-A8T3 
        0.13        15.45        31.27 

$`7P 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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       43.50        20.84         7.36        24.26        33.57        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       90.12        68.52        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.50        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        12.66        16.37         0.03 
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-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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
        9.50        66.94         8.28        32.15        30.25        17.49 
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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        1.08         0.23        19.82        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-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        9.14        12.92        12.46        10.29        19.20         8.78 
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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.13              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            31.27             90.12 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            15.45             15.12 
[1] "0.1 - 31.3 (15.4)" "0.0 - 90.1 (15.1)"
[1] "hr=" "1.5"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  7P LOSS MUTATED         0        0        1         0         2         0
  7P LOSS WILD-TYPE       1        5       14        30       119         5
                   vv
clus                STAGE IV
  7P LOSS MUTATED          0
  7P LOSS WILD-TYPE        5
D53V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               0                30
  STAGE IIB               2               119
  STAGE III               0                 5
  STAGE IV                0                 5
[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 LOSS MUTATED     0   1   2   0
  7P LOSS WILD-TYPE   7  23 145   4
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               0                 7
  T2               1                23
  T3               2               145
  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
  7P LOSS MUTATED     1   2
  7P LOSS WILD-TYPE  49 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    2
  7P LOSS WILD-TYPE   49  127
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               1                49
  1               2               127
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    1  0
  7P LOSS WILD-TYPE 84  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    0
  7P LOSS WILD-TYPE   84    5
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               1                84
  1               0                 5
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   1
  7P LOSS WILD-TYPE  81 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE   81  100
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               2                81
  MALE                 1               100
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   2
  7P LOSS WILD-TYPE 122  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE  122   40
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0               122
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  7P LOSS MUTATED                                     3
  7P LOSS WILD-TYPE                                 150
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  7P LOSS MUTATED                                       0
  7P LOSS WILD-TYPE                                    25
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  7P LOSS MUTATED                                                  0
  7P LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  7P LOSS MUTATED                                     0
  7P LOSS WILD-TYPE                                   1
D53V9, multiclass
                                                  clus
vv                                                 7P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 7P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            150
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           25
  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"
D53V10, continuous
D53V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED     1   1   0   0
  7P LOSS WILD-TYPE 110  52   5   4
D53V12, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               171 
       TCGA-2J-AAB1        TCGA-2J-AAB4        TCGA-2J-AAB6        TCGA-2J-AAB8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-2J-AAB9        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-2J-AABH        TCGA-2J-AABI        TCGA-2J-AABK        TCGA-2J-AABO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-2J-AABP        TCGA-2J-AABR        TCGA-2J-AABT        TCGA-2J-AABU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-2L-AAQI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-2L-AAQJ        TCGA-2L-AAQL        TCGA-2L-AAQM        TCGA-3A-A9I5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-3A-A9I7        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-3A-A9IH        TCGA-3A-A9IJ        TCGA-3A-A9IL        TCGA-3A-A9IN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-3A-A9IO        TCGA-3A-A9IR        TCGA-3A-A9IS        TCGA-3A-A9IU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-3A-A9IV        TCGA-3A-A9IX        TCGA-3A-A9IZ        TCGA-3A-A9J0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F2-6879        TCGA-F2-6880        TCGA-F2-7273        TCGA-F2-7276 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F2-A44G        TCGA-F2-A44H        TCGA-F2-A7TX        TCGA-F2-A8YN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FB-AAPP        TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FB-AAPY        TCGA-FB-AAPZ        TCGA-FB-AAQ0        TCGA-FB-AAQ1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FB-AAQ2        TCGA-FB-AAQ3        TCGA-FB-AAQ6        TCGA-FZ-5920 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FZ-5922        TCGA-FZ-5923        TCGA-FZ-5924        TCGA-FZ-5926 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-H6-8124        TCGA-H8-A6C1        TCGA-HV-A5A6        TCGA-HV-A7OL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HV-A7OP        TCGA-HV-AA8V        TCGA-HV-AA8X        TCGA-HZ-7289 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HZ-7918        TCGA-HZ-7919        TCGA-HZ-7920        TCGA-HZ-7923 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HZ-7924        TCGA-HZ-7925        TCGA-HZ-7926        TCGA-HZ-8001 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HZ-8002        TCGA-HZ-8003        TCGA-HZ-8005        TCGA-HZ-8315 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HZ-8317        TCGA-HZ-8519        TCGA-HZ-8636        TCGA-HZ-8637 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HZ-8638        TCGA-HZ-A49G        TCGA-HZ-A49H        TCGA-HZ-A49I 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HZ-A4BH        TCGA-HZ-A4BK        TCGA-HZ-A77O        TCGA-HZ-A77P 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1        TCGA-HZ-A9TJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7645        TCGA-IB-7646        TCGA-IB-7647 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7652        TCGA-IB-7654 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7888 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-7889        TCGA-IB-7890        TCGA-IB-7891        TCGA-IB-7893 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-7897        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-A5SP        TCGA-IB-A5SQ        TCGA-IB-A5SS        TCGA-IB-A5ST 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7LX        TCGA-IB-A7M4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-AAUM        TCGA-IB-AAUN        TCGA-IB-AAUO        TCGA-IB-AAUP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUR        TCGA-IB-AAUS        TCGA-IB-AAUT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-IB-AAUW        TCGA-L1-A7W4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A8F3        TCGA-LB-A9Q5        TCGA-M8-A5N4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-OE-A75W        TCGA-Q3-A5QY        TCGA-Q3-AA2A        TCGA-RB-A7B8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-RB-AA9M        TCGA-RL-AAAS        TCGA-S4-A8RM        TCGA-S4-A8RO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S4-A8RP        TCGA-US-A774        TCGA-US-A776        TCGA-US-A779 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-US-A77E        TCGA-US-A77G        TCGA-US-A77J        TCGA-XD-AAUG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-XD-AAUH        TCGA-XD-AAUI        TCGA-XD-AAUL        TCGA-XN-A8T5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-YB-A89D        TCGA-YY-A8LH        TCGA-Z5-AAPL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
D53V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       0                         0     3
  7P LOSS WILD-TYPE    11                         7   158
D53V14, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1   2
  7P LOSS WILD-TYPE   4 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    2
  7P LOSS WILD-TYPE    4  134
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               2               134
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    2  2
  7Q LOSS WILD-TYPE 84 94
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               178 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                94 
$`7Q LOSS MUTATED`
TCGA-HV-A5A6 TCGA-HZ-7922 TCGA-PZ-A5RE TCGA-XN-A8T3 
       66.94         0.13        15.45        31.27 

$`7Q 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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       43.50        20.84         7.36        24.26        33.57        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       90.12        68.52        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.50        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        12.66        16.37         0.03 
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-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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 
        9.50         8.28        32.15        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY 
       12.92        12.46        10.29        19.20         8.78        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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        16.37        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.13              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            66.94             90.12 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            23.36             15.09 
[1] "0.1 - 66.9 (23.4)" "0.0 - 90.1 (15.1)"
[1] "hr=" "1.5"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  7Q LOSS MUTATED         0        0        1         0         3         0
  7Q LOSS WILD-TYPE       1        5       14        30       118         5
                   vv
clus                STAGE IV
  7Q LOSS MUTATED          0
  7Q LOSS WILD-TYPE        5
D54V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               0                30
  STAGE IIB               3               118
  STAGE III               0                 5
  STAGE IV                0                 5
[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 LOSS MUTATED     0   1   3   0
  7Q LOSS WILD-TYPE   7  23 144   4
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0                 7
  T2               1                23
  T3               3               144
  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
  7Q LOSS MUTATED     1   3
  7Q LOSS WILD-TYPE  49 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    3
  7Q LOSS WILD-TYPE   49  126
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               1                49
  1               3               126
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    2  0
  7Q LOSS WILD-TYPE 83  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    0
  7Q LOSS WILD-TYPE   83    5
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               2                83
  1               0                 5
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   1
  7Q LOSS WILD-TYPE  80 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    1
  7Q LOSS WILD-TYPE   80  100
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                80
  MALE                 1               100
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   2
  7Q LOSS WILD-TYPE 121  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE  121   40
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1               121
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  7Q LOSS MUTATED                                     4
  7Q LOSS WILD-TYPE                                 149
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  7Q LOSS MUTATED                                       0
  7Q LOSS WILD-TYPE                                    25
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  7Q LOSS MUTATED                                                  0
  7Q LOSS WILD-TYPE                                                4
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  7Q LOSS MUTATED                                     0
  7Q LOSS WILD-TYPE                                   1
D54V9, multiclass
                                                  clus
vv                                                 7Q 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                                                 7Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            149
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           25
  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"
D54V10, continuous
D54V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     2   1   0   0
  7Q LOSS WILD-TYPE 109  52   5   4
D54V12, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               2               109
  R1               1                52
  R2               0                 5
  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"
D54V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       1                         0     3
  7Q LOSS WILD-TYPE    10                         7   158
D54V14, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   2
  7Q LOSS WILD-TYPE   4 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE    4  134
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               2               134
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   16 25
  8P LOSS WILD-TYPE 70 71
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               41               141 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               25                71 
$`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        15.22        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        33.57        90.12        50.70 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-A7DR TCGA-FB-AAPU 
       34.09        24.43        10.98        17.00        11.61        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5926 TCGA-HV-A5A6 TCGA-HZ-7289 
       23.54         5.03         1.02        17.79        66.94        21.73 
TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-A8P1 TCGA-IB-7647 
       19.50        20.19         3.95        17.92         0.23        21.90 
TCGA-IB-7890 TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUQ TCGA-IB-AAUU 
       19.66         8.22        15.88         4.73         6.02         8.05 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-S4-A8RP TCGA-US-A776 
        9.14        12.46         8.78        23.08        39.98 

$`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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU 
       43.50        60.95        68.52        63.85        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6880 TCGA-F2-7273 
       36.26        10.13        75.12        71.74         9.50        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPY 
       16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
        4.21         7.63         9.50         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
       17.49         0.92         7.76         0.13         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        19.59         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-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A9TJ TCGA-IB-7644 
       21.60         5.26        10.85         1.08        19.82        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
       49.38         4.77        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-7891 
       41.33         4.04         3.62        43.79        15.81        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-AAUM 
        7.20        15.12        20.88        21.90         1.35         0.26 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV 
        7.86        14.17        11.11         7.40         9.44        13.28 
TCGA-IB-AAUW TCGA-LB-A7SX TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY 
        7.56        12.92        10.29        19.20        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        24.23        17.26 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.23              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            90.12             75.12 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            17.79             14.47 
[1] "0.2 - 90.1 (17.8)" "0.0 - 75.1 (14.5)"
[1] "hr=" "1"  
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  8P LOSS MUTATED         1        2        4         9        23         1
  8P LOSS WILD-TYPE       0        3       11        21        98         4
                   vv
clus                STAGE IV
  8P LOSS MUTATED          1
  8P LOSS WILD-TYPE        4
D55V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                2                 3
  STAGE IB                4                11
  STAGE IIA               9                21
  STAGE IIB              23                98
  STAGE III               1                 4
  STAGE IV                1                 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 LOSS MUTATED     3   6  32   0
  8P LOSS WILD-TYPE   4  18 115   4
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                 4
  T2               6                18
  T3              32               115
  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"
D55V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    15  24
  8P LOSS WILD-TYPE  35 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     15   24
  8P LOSS WILD-TYPE   35  105
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              15                35
  1              24               105
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   19  1
  8P LOSS WILD-TYPE 66  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     19    1
  8P LOSS WILD-TYPE   66    4
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              19                66
  1               1                 4
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   17 24
  8P LOSS WILD-TYPE 66 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     17   24
  8P LOSS WILD-TYPE   66   77
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              17                66
  MALE                24                77
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   30  7
  8P LOSS WILD-TYPE 92 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     30    7
  8P LOSS WILD-TYPE   92   35
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               30                92
  YES               7                35
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8P LOSS MUTATED                                    33
  8P LOSS WILD-TYPE                                 120
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8P LOSS MUTATED                                       5
  8P LOSS WILD-TYPE                                    20
                   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
D55V9, multiclass
                                                  clus
vv                                                 8P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           33
  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                            120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           20
  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"
D55V10, continuous
D55V11, continuous
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   29 10  1  1
  8P LOSS WILD-TYPE 82 43  4  3
D55V12, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              29                82
  R1              10                43
  R2               1                 4
  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"
D55V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       3                         1    36
  8P LOSS WILD-TYPE     8                         6   125
D55V14, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   3                 8
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  36               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"
D55V15, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0  31
  8P LOSS WILD-TYPE   5 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   31
  8P LOSS WILD-TYPE    5  105
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              31               105
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    7  9
  8Q LOSS WILD-TYPE 79 87
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               166 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9                87 
$`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        90.12        24.43        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        39.98 

$`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        42.31        31.86        15.91        14.47        15.22 
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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
        7.36        24.26        33.57        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        32.81        15.06        36.26        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         9.50        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       13.84        22.06         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 
        8.28        32.15        30.25        17.49         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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-AAUO 
       21.90         1.35         8.22        15.88         0.26         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-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        24.23 
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-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.02              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            90.12             75.12 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           12.035            15.270 
[1] "1.0 - 90.1 (12.0)" "0.0 - 75.1 (15.3)"
[1] "hr=" "1"  
D56V2, 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        5       14        27       110         5
                   vv
clus                STAGE IV
  8Q LOSS MUTATED          0
  8Q LOSS WILD-TYPE        5
D56V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 5
  STAGE IB                1                14
  STAGE IIA               3                27
  STAGE IIB              11               110
  STAGE III               0                 5
  STAGE IV                0                 5
[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   6  22 134   4
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1                 6
  T2               2                22
  T3              13               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"
D56V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     3  11
  8Q LOSS WILD-TYPE  47 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3   11
  8Q LOSS WILD-TYPE   47  118
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               3                47
  1              11               118
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    6  0
  8Q LOSS WILD-TYPE 79  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6    0
  8Q LOSS WILD-TYPE   79    5
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               6                79
  1               0                 5
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    6 10
  8Q LOSS WILD-TYPE 77 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   10
  8Q LOSS WILD-TYPE   77   91
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               6                77
  MALE                10                91
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    13   2
  8Q LOSS WILD-TYPE 109  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     13    2
  8Q LOSS WILD-TYPE  109   40
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               13               109
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8Q LOSS MUTATED                                    12
  8Q LOSS WILD-TYPE                                 141
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8Q LOSS MUTATED                                       2
  8Q LOSS WILD-TYPE                                    23
                   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
D56V9, 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                            141
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           23
  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"
D56V10, continuous
D56V11, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                44 
       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-XN-A8T5        TCGA-YY-A8LH 
"8Q LOSS WILD-TYPE" "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 101  48   5   3
D56V12, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              10               101
  R1               5                48
  R2               0                 5
  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"
D56V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       1                         1    14
  8Q LOSS WILD-TYPE    10                         6   147
D56V14, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   1                10
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  14               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"
D56V15, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  13
  8Q LOSS WILD-TYPE   5 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   13
  8Q LOSS WILD-TYPE    5  123
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              13               123
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   28 46
  9P LOSS WILD-TYPE 58 50
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               74               108 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               46                50 
$`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        42.31        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        24.43        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        12.66        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-HV-A5A3 TCGA-HV-A5A6 TCGA-HV-AA8X TCGA-HZ-7289 
       12.89        22.06         4.21        66.94        17.49        21.73 
TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8005 TCGA-HZ-A49G TCGA-HZ-A4BH 
        0.92         0.13        20.19         3.95        21.70         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 
       21.60         5.26        19.82        49.38        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-8127 TCGA-IB-A5SP 
       23.80        41.33         4.04         3.62        17.16        15.85 
TCGA-IB-A7LX TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-OE-A75W 
        8.22         8.05         9.14        12.92        12.46         8.78 
TCGA-PZ-A5RE TCGA-RB-AA9M TCGA-S4-A8RP TCGA-US-A779 TCGA-XD-AAUI TCGA-XD-AAUL 
       15.45         9.40        23.08        16.80        12.03        16.37 
TCGA-YH-A8SY TCGA-YY-A8LH 
       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 
       15.22        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 
       58.98        43.50        24.26        33.57        60.95        90.12 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A7TX 
       10.13        75.12         9.50        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        16.37         0.03        11.61        15.95        23.54 
TCGA-FZ-5923 TCGA-H6-A45N TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-A7OP 
       20.35        13.84         7.63         9.50         8.28        32.15 
TCGA-HV-AA8V TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
       30.25        19.50         7.76         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        19.59         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A77Q 
       17.92         4.96        16.14        10.13        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7888 
        0.23        12.95         4.77        19.82        15.65        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-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-LB-A9Q5 
       11.11         7.40         9.44        13.28         7.56        10.29 
TCGA-M8-A5N4 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-S4-A8RM 
       19.20        13.68         3.12        15.32         0.30        24.23 
TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       17.26        22.85        39.98        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-Z5-AAPL 
       13.81        12.99        31.27        23.67        11.51        15.35 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            71.74             90.12 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           15.400            15.025 
[1] "0.1 - 71.7 (15.4)" "0.0 - 90.1 (15.0)"
[1] "hr=" "1.3"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  9P LOSS MUTATED         0        1        0        17        53         3
  9P LOSS WILD-TYPE       1        4       15        13        68         2
                   vv
clus                STAGE IV
  9P LOSS MUTATED          1
  9P LOSS WILD-TYPE        4
D57V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 4
  STAGE IB                0                15
  STAGE IIA              17                13
  STAGE IIB              53                68
  STAGE III               3                 2
  STAGE IV                1                 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  5 67  1
  9P LOSS WILD-TYPE  5 19 80  3
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               2                 5
  T2               5                19
  T3              67                80
  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
  9P LOSS MUTATED   18 56
  9P LOSS WILD-TYPE 32 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     18   56
  9P LOSS WILD-TYPE   32   73
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              18                32
  1              56                73
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   33  1
  9P LOSS WILD-TYPE 52  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     33    1
  9P LOSS WILD-TYPE   52    4
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              33                52
  1               1                 4
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   34 41
  9P LOSS WILD-TYPE 49 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     34   41
  9P LOSS WILD-TYPE   49   60
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              34                49
  MALE                41                60
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   47 21
  9P LOSS WILD-TYPE 75 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     47   21
  9P LOSS WILD-TYPE   75   21
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               47                75
  YES              21                21
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9P LOSS MUTATED                                    67
  9P LOSS WILD-TYPE                                  86
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9P LOSS MUTATED                                       7
  9P LOSS WILD-TYPE                                    18
                   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
D57V9, multiclass
                                                  clus
vv                                                 9P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           67
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 9P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             86
  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"
D57V10, continuous
D57V11, continuous
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED   42 22  2  2
  9P LOSS WILD-TYPE 69 31  3  2
D57V12, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              42                69
  R1              22                31
  R2               2                 3
  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"
D57V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       5                         3    64
  9P LOSS WILD-TYPE     6                         4    97
D57V14, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   5                 6
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  64                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    2 52
  9P LOSS WILD-TYPE  3 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   52
  9P LOSS WILD-TYPE    3   84
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              52                84
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   19 23
  9Q LOSS WILD-TYPE 67 73
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               42               140 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23                73 
$`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 
       24.43        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-HZ-A9TJ 
        3.95        21.70         6.38        21.60         5.26        19.82 
TCGA-IB-7645 TCGA-IB-7649 TCGA-IB-A7LX TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
       49.38        15.35         8.22         8.05        12.92        12.46 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH 
       15.45         3.12         9.40        16.37        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        42.31        31.86        15.91        15.22        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 
       58.98        43.50        20.84        24.26        33.57        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       90.12        68.52        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-6880 
       36.26        34.09        10.13        75.12        10.98         9.50 
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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP 
        4.21         7.63         9.50        66.94         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7923 
       30.25        17.49        21.73        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        19.59 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92         4.96        16.14 
TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 
       10.13        10.85         1.08         0.23        12.95         4.77 
TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       21.90        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-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-Q3-A5QY TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RO 
        8.78        13.68        15.32         0.30        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-Z5-AAPL 
       11.51        15.35 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            71.74             90.12 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            13.71             15.27 
[1] "0.1 - 71.7 (13.7)" "0.0 - 90.1 (15.3)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  9Q LOSS MUTATED         0        1        1         8        29         3
  9Q LOSS WILD-TYPE       1        4       14        22        92         2
                   vv
clus                STAGE IV
  9Q LOSS MUTATED          1
  9Q LOSS WILD-TYPE        4
D58V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 4
  STAGE IB                1                14
  STAGE IIA               8                22
  STAGE IIB              29                92
  STAGE III               3                 2
  STAGE IV                1                 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  36   1
  9Q LOSS WILD-TYPE   5  20 111   3
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               2                 5
  T2               4                20
  T3              36               111
  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"
D58V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   10 33
  9Q LOSS WILD-TYPE 40 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     10   33
  9Q LOSS WILD-TYPE   40   96
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              10                40
  1              33                96
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   14  1
  9Q LOSS WILD-TYPE 71  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     14    1
  9Q LOSS WILD-TYPE   71    4
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              14                71
  1               1                 4
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   20 23
  9Q LOSS WILD-TYPE 63 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     20   23
  9Q LOSS WILD-TYPE   63   78
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              20                63
  MALE                23                78
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   23 15
  9Q LOSS WILD-TYPE 99 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     23   15
  9Q LOSS WILD-TYPE   99   27
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               23                99
  YES              15                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9Q LOSS MUTATED                                    39
  9Q LOSS WILD-TYPE                                 114
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9Q LOSS MUTATED                                       3
  9Q LOSS WILD-TYPE                                    22
                   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
D58V9, multiclass
                                                  clus
vv                                                 9Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           39
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 9Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            114
  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"
D58V10, continuous
D58V11, continuous
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED   26 11  0  1
  9Q LOSS WILD-TYPE 85 42  5  3
D58V12, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              26                85
  R1              11                42
  R2               0                 5
  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"
D58V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         2    38
  9Q LOSS WILD-TYPE    11                         5   123
D58V14, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   0                11
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  38               123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  32
  9Q LOSS WILD-TYPE   3 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   32
  9Q LOSS WILD-TYPE    3  104
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              32               104
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   14 21
  10P LOSS WILD-TYPE 72 75
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                35                147 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                21                 75 
$`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        15.22         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        90.12        32.81        15.06        12.66 
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-HV-A5A6 TCGA-HZ-7289 TCGA-HZ-8005 TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7646 
       66.94        21.73         3.95         5.26         1.08         4.77 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-A5SQ TCGA-IB-A6UG 
       41.33         4.04        19.66         3.85         7.20         1.35 
TCGA-IB-A7LX TCGA-IB-AAUN TCGA-S4-A8RO TCGA-XD-AAUG TCGA-XN-A8T3 
        8.22         4.73        17.26        13.81        31.27 

$`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        42.31        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO 
       20.84         7.36        33.57        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        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 
       15.78        17.79        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
        9.50         8.28        32.15        30.25        17.49         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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        6.38        21.60        10.85         0.23        19.82        12.95 
TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
       49.38        21.90        15.35        19.82        23.80        15.65 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 
        3.62        43.79        15.81        21.30        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       17.16        12.00        15.85        15.12        20.88        21.90 
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-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        24.23 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D 
       18.67        12.99        12.03        16.37        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.08               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             90.12              75.12 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             14.47              15.35 
[1] "1.1 - 90.1 (14.5)" "0.0 - 75.1 (15.3)"
[1] "hr=" "1.2"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  10P LOSS MUTATED         1        0        5         2        26         0
  10P LOSS WILD-TYPE       0        5       10        28        95         5
                    vv
clus                 STAGE IV
  10P LOSS MUTATED          2
  10P LOSS WILD-TYPE        3
D59V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 5                 10
  STAGE IIA                2                 28
  STAGE IIB               26                 95
  STAGE III                0                  5
  STAGE IV                 2                  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
  10P LOSS MUTATED     1   7  27   1
  10P LOSS WILD-TYPE   6  17 120   3
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                1                  6
  T2                7                 17
  T3               27                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"
D59V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     7  28
  10P LOSS WILD-TYPE  43 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7   28
  10P LOSS WILD-TYPE   43  101
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                7                 43
  1               28                101
[1] 2 2
[1] FALSE
D59V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   18  2
  10P LOSS WILD-TYPE 67  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     18    2
  10P LOSS WILD-TYPE   67    3
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               18                 67
  1                2                  3
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   16 20
  10P LOSS WILD-TYPE 67 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     16   20
  10P LOSS WILD-TYPE   67   81
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               16                 67
  MALE                 20                 81
[1] 2 2
[1] FALSE
D59V8, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   25  9
  10P LOSS WILD-TYPE 97 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     25    9
  10P LOSS WILD-TYPE   97   33
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                25                 97
  YES                9                 33
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10P LOSS MUTATED                                    29
  10P LOSS WILD-TYPE                                 124
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10P LOSS MUTATED                                       6
  10P LOSS WILD-TYPE                                    19
                    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
D59V9, multiclass
                                                  clus
vv                                                 10P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            29
  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                             124
  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"
D59V10, continuous
D59V11, continuous
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED   22 11  0  1
  10P LOSS WILD-TYPE 89 42  5  3
D59V12, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               22                 89
  R1               11                 42
  R2                0                  5
  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"
D59V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       1                         0    33
  10P LOSS WILD-TYPE    10                         7   128
D59V14, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   33                128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V15, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  25
  10P LOSS WILD-TYPE   4 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   25
  10P LOSS WILD-TYPE    4  111
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               25                111
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   15 15
  10Q LOSS WILD-TYPE 71 81
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                30                152 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                 81 
$`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        15.22         9.11         3.39        45.47 
TCGA-3A-A9IL TCGA-3A-A9IS TCGA-3A-A9IU TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAQ2 
       90.12        32.81        15.06        12.66        15.95         5.03 
TCGA-FZ-5921 TCGA-H6-8124 TCGA-HV-A5A6 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-8005 
        5.10        12.89        66.94        21.73         0.92         3.95 
TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A9TJ TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7887 
        5.26         1.08        19.82         4.77        41.33         3.62 
TCGA-IB-7890 TCGA-IB-7893 TCGA-S4-A8RO TCGA-US-A776 TCGA-XD-AAUG TCGA-XN-A8T3 
       19.66         3.85        17.26        39.98        13.81        31.27 

$`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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ 
       43.50        20.84         7.36        24.26        33.57        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        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 
       24.43        75.12        71.74        10.98         9.50        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 
       16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL 
       13.84        22.06         4.21         7.63         9.50         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       32.15        30.25        17.49        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 
       19.59         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-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-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 
       23.80        15.65         4.04        43.79        15.81        21.30 
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-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        24.23 
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-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        16.37        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.92               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             90.12              75.12 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            14.765             15.335 
[1] "0.9 - 90.1 (14.8)" "0.0 - 75.1 (15.3)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  10Q LOSS MUTATED         1        0        3         2        22         0
  10Q LOSS WILD-TYPE       0        5       12        28        99         5
                    vv
clus                 STAGE IV
  10Q LOSS MUTATED          2
  10Q LOSS WILD-TYPE        3
D60V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 3                 12
  STAGE IIA                2                 28
  STAGE IIB               22                 99
  STAGE III                0                  5
  STAGE IV                 2                  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   4  25   0
  10Q LOSS WILD-TYPE   6  20 122   4
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                1                  6
  T2                4                 20
  T3               25                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"
D60V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6  23
  10Q LOSS WILD-TYPE  44 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   23
  10Q LOSS WILD-TYPE   44  106
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                6                 44
  1               23                106
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   15  2
  10Q LOSS WILD-TYPE 70  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15    2
  10Q LOSS WILD-TYPE   70    3
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               15                 70
  1                2                  3
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   13 17
  10Q LOSS WILD-TYPE 70 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     13   17
  10Q LOSS WILD-TYPE   70   84
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               13                 70
  MALE                 17                 84
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    21   7
  10Q LOSS WILD-TYPE 101  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     21    7
  10Q LOSS WILD-TYPE  101   35
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                21                101
  YES                7                 35
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10Q LOSS MUTATED                                    22
  10Q LOSS WILD-TYPE                                 131
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10Q LOSS MUTATED                                       6
  10Q LOSS WILD-TYPE                                    19
                    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
D60V9, multiclass
                                                  clus
vv                                                 10Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 10Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             131
  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"
D60V10, continuous
D60V11, continuous
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED   18  9  0  1
  10Q LOSS WILD-TYPE 93 44  5  3
D60V12, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               18                 93
  R1                9                 44
  R2                0                  5
  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"
D60V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       1                         0    27
  10Q LOSS WILD-TYPE    10                         7   134
D60V14, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   27                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"
D60V15, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  20
  10Q LOSS WILD-TYPE   4 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   20
  10Q LOSS WILD-TYPE    4  116
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               20                116
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   11  6
  11P LOSS WILD-TYPE 75 90
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                17                165 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 90 
$`11P LOSS MUTATED`
TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IS TCGA-3A-A9J0 TCGA-F2-A44H TCGA-FB-AAPP 
       45.47        90.12        32.81        24.43        19.27        15.95 
TCGA-FB-AAPZ TCGA-FZ-5924 TCGA-HV-A7OP TCGA-HZ-7918 TCGA-IB-7652 TCGA-IB-7886 
       23.54        15.78        32.15         0.92        23.80         4.04 
TCGA-IB-7889 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUI TCGA-XN-A8T3 
       15.81        12.92        17.26        12.03        31.27 

$`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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN 
       20.84         7.36        24.26        33.57        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        36.26        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         9.50        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        12.66        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       13.84        22.06         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7920 
        8.28        30.25        17.49        21.73        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-7890 TCGA-IB-7891 
       15.65        41.33         3.62        43.79        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-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        24.23 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D 
       18.67        13.81        12.99        16.37        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.92               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             90.12              75.12 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             19.27              14.40 
[1] "0.9 - 90.1 (19.3)" "0.0 - 75.1 (14.4)"
[1] "hr=" "2.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  11P LOSS MUTATED         1        0        2         2        12         0
  11P LOSS WILD-TYPE       0        5       13        28       109         5
                    vv
clus                 STAGE IV
  11P LOSS MUTATED          0
  11P LOSS WILD-TYPE        5
D61V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA                2                 28
  STAGE IIB               12                109
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   3  13   0
  11P LOSS WILD-TYPE   6  21 134   4
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                  6
  T2                3                 21
  T3               13                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"
D61V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     3  13
  11P LOSS WILD-TYPE  47 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3   13
  11P LOSS WILD-TYPE   47  116
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                3                 47
  1               13                116
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    8  0
  11P LOSS WILD-TYPE 77  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8    0
  11P LOSS WILD-TYPE   77    5
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                8                 77
  1                0                  5
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    6 11
  11P LOSS WILD-TYPE 77 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6   11
  11P LOSS WILD-TYPE   77   90
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                6                 77
  MALE                 11                 90
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    11   5
  11P LOSS WILD-TYPE 111  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     11    5
  11P LOSS WILD-TYPE  111   37
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                11                111
  YES                5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11P LOSS MUTATED                                    13
  11P LOSS WILD-TYPE                                 140
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11P LOSS MUTATED                                       4
  11P LOSS WILD-TYPE                                    21
                    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
D61V9, multiclass
                                                  clus
vv                                                 11P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 11P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             140
  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"
D61V10, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 54 
        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-HV-AA8V         TCGA-HZ-A77Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8126 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-IB-AAUU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-XN-A8T5         TCGA-YY-A8LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D61V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    10   7   0   0
  11P LOSS WILD-TYPE 101  46   5   4
D61V12, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               10                101
  R1                7                 46
  R2                0                  5
  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"
D61V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       2                         1    14
  11P LOSS WILD-TYPE     9                         6   147
D61V14, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    2                  9
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   14                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"
D61V15, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1  14
  11P LOSS WILD-TYPE   4 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1   14
  11P LOSS WILD-TYPE    4  122
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               14                122
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   11  5
  11Q LOSS WILD-TYPE 75 91
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                166 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 91 
$`11Q LOSS MUTATED`
TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IS TCGA-3A-A9J0 TCGA-F2-A44H TCGA-FB-A78T 
       45.47        90.12        32.81        24.43        19.27         0.03 
TCGA-FB-AAPP TCGA-FZ-5924 TCGA-HV-A7OP TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-A77P 
       15.95        15.78        32.15        21.73         0.92        10.85 
TCGA-LB-A7SX TCGA-US-A776 TCGA-XD-AAUI TCGA-XN-A8T3 
       12.92        39.98        12.03        31.27 

$`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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN 
       20.84         7.36        24.26        33.57        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        36.26        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         9.50        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        12.66        16.37 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       13.84        22.06         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
        8.28        30.25        17.49        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 
       19.59         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-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
        5.26         1.08         0.23        19.82        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-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
        7.56         9.14        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 
       24.23        17.26        23.08        22.85        16.80        14.14 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL TCGA-XN-A8T5 
        0.39        18.67        13.81        12.99        16.37        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.13 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             90.12              75.12 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              20.5               14.7 
[1] "0.0 - 90.1 (20.5)" "0.1 - 75.1 (14.7)"
[1] "hr=" "2.5"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  11Q LOSS MUTATED         1        0        2         3        10         0
  11Q LOSS WILD-TYPE       0        5       13        27       111         5
                    vv
clus                 STAGE IV
  11Q LOSS MUTATED          0
  11Q LOSS WILD-TYPE        5
D62V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA                3                 27
  STAGE IIB               10                111
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   2  13   0
  11Q LOSS WILD-TYPE   6  22 134   4
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                  6
  T2                2                 22
  T3               13                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"
D62V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     4  11
  11Q LOSS WILD-TYPE  46 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4   11
  11Q LOSS WILD-TYPE   46  118
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                4                 46
  1               11                118
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    6  0
  11Q LOSS WILD-TYPE 79  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6    0
  11Q LOSS WILD-TYPE   79    5
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                6                 79
  1                0                  5
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    4 12
  11Q LOSS WILD-TYPE 79 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4   12
  11Q LOSS WILD-TYPE   79   89
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                4                 79
  MALE                 12                 89
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    10   4
  11Q LOSS WILD-TYPE 112  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     10    4
  11Q LOSS WILD-TYPE  112   38
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                10                112
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11Q LOSS MUTATED                                     9
  11Q LOSS WILD-TYPE                                 144
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11Q LOSS MUTATED                                       6
  11Q LOSS WILD-TYPE                                    19
                    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
D62V9, multiclass
                                                  clus
vv                                                 11Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 11Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             144
  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"
D62V10, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 54 
        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-HV-AA8V         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7886 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8126 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-IB-AAUU 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-XN-A8T5         TCGA-YY-A8LH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D62V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    11   4   0   1
  11Q LOSS WILD-TYPE 100  49   5   3
D62V12, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               11                100
  R1                4                 49
  R2                0                  5
  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"
D62V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       1                         1    14
  11Q LOSS WILD-TYPE    10                         6   147
D62V14, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   14                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"
D62V15, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  13
  11Q LOSS WILD-TYPE   4 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   13
  11Q LOSS WILD-TYPE    4  123
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               13                123
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   10 10
  12P LOSS WILD-TYPE 76 86
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                20                162 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                10                 86 
$`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        15.22        22.49        24.26        33.57 
TCGA-3A-A9J0 TCGA-F2-A8YN TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FZ-5920 TCGA-HV-A7OP 
       24.43        17.00        11.61        37.15         2.01        32.15 
TCGA-HV-AA8V TCGA-HZ-7919 TCGA-HZ-8636 TCGA-IB-7886 TCGA-IB-7893 TCGA-IB-A5SP 
       30.25        19.50        17.92         4.04         3.85        15.85 
TCGA-IB-AAUU TCGA-LB-A7SX 
        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 
       42.31        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        58.98        43.50        20.84         7.36        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       90.12        68.52        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       36.26        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 
        9.50        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        12.66        16.37         0.03        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-HV-A5A3 
       15.78        17.79        12.89        13.84        22.06         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8X TCGA-HZ-7289 
        7.63         9.50        66.94         8.28        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        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-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-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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              2.01               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             37.15              90.12 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             17.46              14.70 
[1] "2.0 - 37.1 (17.5)" "0.0 - 90.1 (14.7)"
[1] "hr=" "1.2"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  12P LOSS MUTATED         0        1        0         4        14         0
  12P LOSS WILD-TYPE       1        4       15        26       107         5
                    vv
clus                 STAGE IV
  12P LOSS MUTATED          1
  12P LOSS WILD-TYPE        4
D63V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  4
  STAGE IB                 0                 15
  STAGE IIA                4                 26
  STAGE IIB               14                107
  STAGE III                0                  5
  STAGE IV                 1                  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 LOSS MUTATED     1   1  18   0
  12P LOSS WILD-TYPE   6  23 129   4
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                  6
  T2                1                 23
  T3               18                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"
D63V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  14
  12P LOSS WILD-TYPE  45 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   14
  12P LOSS WILD-TYPE   45  115
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                5                 45
  1               14                115
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   13  1
  12P LOSS WILD-TYPE 72  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     13    1
  12P LOSS WILD-TYPE   72    4
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               13                 72
  1                1                  4
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    6 14
  12P LOSS WILD-TYPE 77 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6   14
  12P LOSS WILD-TYPE   77   87
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                6                 77
  MALE                 14                 87
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    15   2
  12P LOSS WILD-TYPE 107  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     15    2
  12P LOSS WILD-TYPE  107   40
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                15                107
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12P LOSS MUTATED                                    16
  12P LOSS WILD-TYPE                                 137
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12P LOSS MUTATED                                       2
  12P LOSS WILD-TYPE                                    23
                    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
D63V9, multiclass
                                                  clus
vv                                                 12P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            16
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 12P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             137
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            23
  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"
D63V10, continuous
D63V11, continuous
                    vv
clus                 R0 R1 R2 RX
  12P LOSS MUTATED   12  7  1  0
  12P LOSS WILD-TYPE 99 46  4  4
D63V12, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               12                 99
  R1                7                 46
  R2                1                  4
  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"
D63V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       3                         2    15
  12P LOSS WILD-TYPE     8                         5   146
D63V14, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    3                  8
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   15                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"
D63V15, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  13
  12P LOSS WILD-TYPE   5 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   13
  12P LOSS WILD-TYPE    5  123
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               13                123
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED   12 16
  12Q LOSS WILD-TYPE 74 80
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                28                154 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                16                 80 
$`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        42.31        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        33.57        24.43        11.61         5.03         2.01 
TCGA-FZ-5924 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-8636 TCGA-HZ-A77O 
       15.78        32.15        30.25        17.49        17.92         5.26 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 
       19.82        23.80         4.04         3.62        19.66         3.85 
TCGA-IB-AAUN TCGA-IB-AAUU TCGA-LB-A7SX TCGA-YH-A8SY 
        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        15.22        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
       43.50        20.84         7.36        60.95        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        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         9.50        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 
       12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
       12.89        13.84        22.06         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       66.94         8.28        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        19.59         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-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-7654 TCGA-IB-7885 TCGA-IB-7888 
       21.90        15.35        19.82        15.65        41.33        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-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-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22        15.88         0.26         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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
       18.67        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        66.28        15.35 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              2.01               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             42.31              90.12 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            16.635             15.090 
[1] "2.0 - 42.3 (16.6)" "0.0 - 90.1 (15.1)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  12Q LOSS MUTATED         0        1        2         5        17         1
  12Q LOSS WILD-TYPE       1        4       13        25       104         4
                    vv
clus                 STAGE IV
  12Q LOSS MUTATED          2
  12Q LOSS WILD-TYPE        3
D64V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  4
  STAGE IB                 2                 13
  STAGE IIA                5                 25
  STAGE IIB               17                104
  STAGE III                1                  4
  STAGE IV                 2                  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   5  22   0
  12Q LOSS WILD-TYPE   6  19 125   4
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                  6
  T2                5                 19
  T3               22                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"
D64V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     8  19
  12Q LOSS WILD-TYPE  42 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8   19
  12Q LOSS WILD-TYPE   42  110
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                8                 42
  1               19                110
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   16  2
  12Q LOSS WILD-TYPE 69  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     16    2
  12Q LOSS WILD-TYPE   69    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               16                 69
  1                2                  3
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   12 16
  12Q LOSS WILD-TYPE 71 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     12   16
  12Q LOSS WILD-TYPE   71   85
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               12                 71
  MALE                 16                 85
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    22   4
  12Q LOSS WILD-TYPE 100  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     22    4
  12Q LOSS WILD-TYPE  100   38
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                22                100
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12Q LOSS MUTATED                                    21
  12Q LOSS WILD-TYPE                                 132
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12Q LOSS MUTATED                                       5
  12Q LOSS WILD-TYPE                                    20
                    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
D64V9, multiclass
                                                  clus
vv                                                 12Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 12Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             132
  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"
D64V10, continuous
D64V11, continuous
                    vv
clus                 R0 R1 R2 RX
  12Q LOSS MUTATED   16  9  2  0
  12Q LOSS WILD-TYPE 95 44  3  4
D64V12, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               16                 95
  R1                9                 44
  R2                2                  3
  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"
D64V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       5                         2    20
  12Q LOSS WILD-TYPE     6                         5   141
D64V14, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    5                  6
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   20                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"
D64V15, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  18
  12Q LOSS WILD-TYPE   5 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   18
  12Q LOSS WILD-TYPE    5  118
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               18                118
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    6 14
  13Q LOSS WILD-TYPE 80 82
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                162 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                 82 
$`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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       15.22        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        58.98        43.50        20.84 
TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IS 
       33.57        60.95        90.12        68.52        63.85        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        34.09        24.43        75.12        71.74 
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
       10.98         9.50        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        12.66        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       13.84        22.06         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7920 
        8.28        32.15        30.25        17.49        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        19.59         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-A77O 
        4.96        21.70        16.14        10.13         6.38         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        12.95        49.38 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7887 
       21.90        15.35        19.82        23.80        15.65         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-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
        2.47        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22         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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.92               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             50.70              90.12 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            14.035             15.270 
[1] "0.9 - 50.7 (14.0)" "0.0 - 90.1 (15.3)"
[1] "hr=" "1.6"
D65V2, 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        5       14        30       104         4
                    vv
clus                 STAGE IV
  13Q LOSS MUTATED          1
  13Q LOSS WILD-TYPE        4
D65V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 1                 14
  STAGE IIA                0                 30
  STAGE IIB               17                104
  STAGE III                1                  4
  STAGE IV                 1                  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 LOSS MUTATED     0   1  18   1
  13Q LOSS WILD-TYPE   7  23 129   3
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                0                  7
  T2                1                 23
  T3               18                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"
D65V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     3  17
  13Q LOSS WILD-TYPE  47 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3   17
  13Q LOSS WILD-TYPE   47  112
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                3                 47
  1               17                112
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9  1
  13Q LOSS WILD-TYPE 76  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    1
  13Q LOSS WILD-TYPE   76    4
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                9                 76
  1                1                  4
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9 11
  13Q LOSS WILD-TYPE 74 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   11
  13Q LOSS WILD-TYPE   74   90
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                 74
  MALE                 11                 90
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    15   3
  13Q LOSS WILD-TYPE 107  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     15    3
  13Q LOSS WILD-TYPE  107   39
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                15                107
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  13Q LOSS MUTATED                                    17
  13Q LOSS WILD-TYPE                                 136
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  13Q LOSS MUTATED                                       3
  13Q LOSS WILD-TYPE                                    22
                    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
D65V9, 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                             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"
D65V10, continuous
D65V11, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    10   8   1   1
  13Q LOSS WILD-TYPE 101  45   4   3
D65V12, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               10                101
  R1                8                 45
  R2                1                  4
  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"
D65V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         2    18
  13Q LOSS WILD-TYPE    11                         5   143
D65V14, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   18                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"
D65V15, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  17
  13Q LOSS WILD-TYPE   4 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   17
  13Q LOSS WILD-TYPE    4  119
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               17                119
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    6 10
  14Q LOSS WILD-TYPE 80 86
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                166 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                10                 86 
$`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        33.57        24.43 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-HV-A5A6 TCGA-HV-A7OP TCGA-HZ-8005 TCGA-IB-7647 
       16.37        11.61        66.94        32.15         3.95        21.90 
TCGA-IB-AAUN TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-YH-A8SY 
        4.73        12.92        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        42.31        15.91        14.47        15.22        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        58.98        43.50        20.84         7.36 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        90.12        68.52        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        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         9.50        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        12.66         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL 
       13.84        22.06         4.21         7.63         9.50         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
       49.38         4.77        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-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22        15.88         0.26         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-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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
       18.67        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        66.28        15.35 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              3.95               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             66.94              90.12 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            18.165             15.090 
[1] "4.0 - 66.9 (18.2)" "0.0 - 90.1 (15.1)"
[1] "hr=" "1"  
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  14Q LOSS MUTATED         0        1        2         3         9         1
  14Q LOSS WILD-TYPE       1        4       13        27       112         4
                    vv
clus                 STAGE IV
  14Q LOSS MUTATED          0
  14Q LOSS WILD-TYPE        5
D66V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  4
  STAGE IB                 2                 13
  STAGE IIA                3                 27
  STAGE IIB                9                112
  STAGE III                1                  4
  STAGE IV                 0                  5
[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  13   0
  14Q LOSS WILD-TYPE   6  22 134   4
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                1                  6
  T2                2                 22
  T3               13                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"
D66V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     5  10
  14Q LOSS WILD-TYPE  45 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5   10
  14Q LOSS WILD-TYPE   45  119
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0                5                 45
  1               10                119
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    8  0
  14Q LOSS WILD-TYPE 77  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      8    0
  14Q LOSS WILD-TYPE   77    5
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0                8                 77
  1                0                  5
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    8  8
  14Q LOSS WILD-TYPE 75 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      8    8
  14Q LOSS WILD-TYPE   75   93
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                8                 75
  MALE                  8                 93
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    11   5
  14Q LOSS WILD-TYPE 111  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11    5
  14Q LOSS WILD-TYPE  111   37
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                11                111
  YES                5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  14Q LOSS MUTATED                                    12
  14Q LOSS WILD-TYPE                                 141
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  14Q LOSS MUTATED                                       2
  14Q LOSS WILD-TYPE                                    23
                    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
D66V9, multiclass
                                                  clus
vv                                                 14Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 14Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             141
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            23
  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"
D66V10, continuous
D66V11, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED     9   5   0   1
  14Q LOSS WILD-TYPE 102  48   5   3
D66V12, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0                9                102
  R1                5                 48
  R2                0                  5
  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"
D66V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       3                         2    11
  14Q LOSS WILD-TYPE     8                         5   150
D66V14, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    3                  8
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   11                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"
D66V15, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     0  11
  14Q LOSS WILD-TYPE   5 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   11
  14Q LOSS WILD-TYPE    5  125
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               11                125
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   16 14
  15Q LOSS WILD-TYPE 70 82
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                30                152 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                14                 82 
$`15Q LOSS MUTATED`
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABP TCGA-2J-AABT TCGA-3A-A9IB TCGA-3A-A9IS 
       22.22        42.31        15.22        10.49         7.36        32.81 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A7DR TCGA-FB-AAPP 
       71.74        10.98        17.00        12.66        11.61        15.95 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-HV-A5A3 TCGA-HV-A5A6 TCGA-HV-A7OP 
       23.54        15.55         5.03         4.21        66.94        32.15 
TCGA-HZ-8005 TCGA-HZ-A4BK TCGA-IB-7644 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 
        3.95        21.60        12.95        19.66         3.85        17.16 
TCGA-IB-A5SP TCGA-IB-A7M4 TCGA-M8-A5N4 TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YH-A8SY 
       15.85        15.88        19.20        12.03        31.27        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        58.98        43.50        20.84        24.26        33.57 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU 
       60.95        90.12        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 
       36.26        34.09        10.13        24.43        75.12         9.50 
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 
       16.37         0.03        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-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       22.06         7.63         9.50         8.28        30.25        17.49 
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        19.59 
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-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       16.14        10.13         6.38         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        0.23        19.82        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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D 
       18.67        13.81        12.99        16.37        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              3.85               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             71.74              90.12 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            15.865             14.700 
[1] "3.9 - 71.7 (15.9)" "0.0 - 90.1 (14.7)"
[1] "hr=" "1.3"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  15Q LOSS MUTATED         0        0        3        10        15         1
  15Q LOSS WILD-TYPE       1        5       12        20       106         4
                    vv
clus                 STAGE IV
  15Q LOSS MUTATED          1
  15Q LOSS WILD-TYPE        4
D67V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 3                 12
  STAGE IIA               10                 20
  STAGE IIB               15                106
  STAGE III                1                  4
  STAGE IV                 1                  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 LOSS MUTATED     0   4  26   0
  15Q LOSS WILD-TYPE   7  20 121   4
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                0                  7
  T2                4                 20
  T3               26                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"
D67V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    11  17
  15Q LOSS WILD-TYPE  39 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     11   17
  15Q LOSS WILD-TYPE   39  112
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               11                 39
  1               17                112
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   16  1
  15Q LOSS WILD-TYPE 69  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     16    1
  15Q LOSS WILD-TYPE   69    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               16                 69
  1                1                  4
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   10 20
  15Q LOSS WILD-TYPE 73 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     10   20
  15Q LOSS WILD-TYPE   73   81
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               10                 73
  MALE                 20                 81
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20   8
  15Q LOSS WILD-TYPE 102  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20    8
  15Q LOSS WILD-TYPE  102   34
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                20                102
  YES                8                 34
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  15Q LOSS MUTATED                                    22
  15Q LOSS WILD-TYPE                                 131
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  15Q LOSS MUTATED                                       5
  15Q LOSS WILD-TYPE                                    20
                    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
D67V9, multiclass
                                                  clus
vv                                                 15Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 15Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             131
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            20
  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"
D67V10, continuous
D67V11, continuous
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   16 10  0  0
  15Q LOSS WILD-TYPE 95 43  5  4
D67V12, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               16                 95
  R1               10                 43
  R2                0                  5
  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"
D67V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       4                         0    24
  15Q LOSS WILD-TYPE     7                         7   137
D67V14, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    4                  7
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   24                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"
D67V15, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2  17
  15Q LOSS WILD-TYPE   3 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   17
  15Q LOSS WILD-TYPE    3  119
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               17                119
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    9  2
  16P LOSS WILD-TYPE 77 94
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                171 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 94 
$`16P LOSS MUTATED`
TCGA-2J-AABA TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9IL TCGA-3A-A9IS TCGA-FB-A545 
       19.96        15.22        45.47        90.12        32.81        12.66 
TCGA-FB-AAPZ TCGA-HV-A7OP TCGA-HZ-A4BK TCGA-IB-A7LX TCGA-XN-A8T3 
       23.54        32.15        21.60         8.22        31.27 

$`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        42.31        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        58.98        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        33.57        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        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
       12.89        13.84        22.06         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 
       66.94         8.28        30.25        17.49        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        19.59         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-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
       10.13         6.38         5.26        10.85         1.08         0.23 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        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-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         1.35        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
       22.85        39.98        16.80        14.14         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        16.37        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              8.22               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             90.12              75.12 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             23.54              14.47 
[1] "8.2 - 90.1 (23.5)" "0.0 - 75.1 (14.5)"
[1] "hr=" "5.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  16P LOSS MUTATED         1        0        2         0         8         0
  16P LOSS WILD-TYPE       0        5       13        30       113         5
                    vv
clus                 STAGE IV
  16P LOSS MUTATED          0
  16P LOSS WILD-TYPE        5
D68V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA                0                 30
  STAGE IIB                8                113
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   3   7   0
  16P LOSS WILD-TYPE   6  21 140   4
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                1                  6
  T2                3                 21
  T3                7                140
  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"
D68V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     2   8
  16P LOSS WILD-TYPE  48 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    8
  16P LOSS WILD-TYPE   48  121
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                2                 48
  1                8                121
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    5  0
  16P LOSS WILD-TYPE 80  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    0
  16P LOSS WILD-TYPE   80    5
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                5                 80
  1                0                  5
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3  8
  16P LOSS WILD-TYPE 80 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    8
  16P LOSS WILD-TYPE   80   93
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 80
  MALE                  8                 93
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7   4
  16P LOSS WILD-TYPE 115  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    4
  16P LOSS WILD-TYPE  115   38
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 7                115
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16P LOSS MUTATED                                     5
  16P LOSS WILD-TYPE                                 148
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16P LOSS MUTATED                                       5
  16P LOSS WILD-TYPE                                    20
                    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
D68V9, multiclass
                                                  clus
vv                                                 16P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 16P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             148
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            20
  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"
D68V10, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 55 
        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-HV-AA8V         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-7886 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8126 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-IB-AAUU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A7SX         TCGA-LB-A9Q5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RM         TCGA-S4-A8RP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUL         TCGA-XN-A8T5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-YY-A8LH 
"16P LOSS WILD-TYPE" 
D68V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED     6   4   0   0
  16P LOSS WILD-TYPE 105  49   5   4
D68V12, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                6                105
  R1                4                 49
  R2                0                  5
  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"
D68V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         0    10
  16P LOSS WILD-TYPE    10                         7   151
D68V14, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   10                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"
D68V15, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1   6
  16P LOSS WILD-TYPE   4 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    6
  16P LOSS WILD-TYPE    4  130
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                6                130
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    7  6
  16Q LOSS WILD-TYPE 79 90
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                169 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                 90 
$`16Q LOSS MUTATED`
TCGA-2J-AABA TCGA-2J-AABP TCGA-2L-AAQE TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IC 
       19.96        15.22        22.49         9.60        45.47        24.26 
TCGA-3A-A9IL TCGA-3A-A9IS TCGA-HV-A5A4 TCGA-HV-A7OP TCGA-HZ-7289 TCGA-IB-A7LX 
       90.12        32.81         7.63        32.15        21.73         8.22 
TCGA-XN-A8T3 
       31.27 

$`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        42.31        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 
       58.98        43.50        20.84         7.36        33.57        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        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84        22.06         4.21         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       30.25        17.49         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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        16.37        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              7.63               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             90.12              75.12 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             22.49              14.47 
[1] "7.6 - 90.1 (22.5)" "0.0 - 75.1 (14.5)"
[1] "hr=" "1.9"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  16Q LOSS MUTATED         1        0        2         1         9         0
  16Q LOSS WILD-TYPE       0        5       13        29       112         5
                    vv
clus                 STAGE IV
  16Q LOSS MUTATED          0
  16Q LOSS WILD-TYPE        5
D69V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA                1                 29
  STAGE IIB                9                112
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   2  10   0
  16Q LOSS WILD-TYPE   6  22 137   4
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                1                  6
  T2                2                 22
  T3               10                137
  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
  16Q LOSS MUTATED     3   9
  16Q LOSS WILD-TYPE  47 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    9
  16Q LOSS WILD-TYPE   47  120
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                3                 47
  1                9                120
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    5  0
  16Q LOSS WILD-TYPE 80  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    0
  16Q LOSS WILD-TYPE   80    5
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                5                 80
  1                0                  5
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  9
  16Q LOSS WILD-TYPE 79 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    9
  16Q LOSS WILD-TYPE   79   92
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                 79
  MALE                  9                 92
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    10   3
  16Q LOSS WILD-TYPE 112  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     10    3
  16Q LOSS WILD-TYPE  112   39
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                10                112
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16Q LOSS MUTATED                                     7
  16Q LOSS WILD-TYPE                                 146
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16Q LOSS MUTATED                                       5
  16Q LOSS WILD-TYPE                                    20
                    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
D69V9, multiclass
                                                  clus
vv                                                 16Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 16Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             146
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            20
  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"
D69V10, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 54 
        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-HV-AA8V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UF         TCGA-IB-A6UG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IB-AAUT         TCGA-IB-AAUU         TCGA-IB-AAUV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-XN-A8T5         TCGA-YY-A8LH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D69V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED     7   3   0   2
  16Q LOSS WILD-TYPE 104  50   5   2
D69V12, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0                7                104
  R1                3                 50
  R2                0                  5
  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"
D69V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       2                         0    11
  16Q LOSS WILD-TYPE     9                         7   150
D69V14, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    2                  9
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   11                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"
D69V15, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1   5
  16Q LOSS WILD-TYPE   4 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    5
  16Q LOSS WILD-TYPE    4  131
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                5                131
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   31 49
  17P LOSS WILD-TYPE 55 47
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                80                102 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                49                 47 
$`17P LOSS MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABT 
       23.97        42.31        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        33.57        15.06        10.13 
TCGA-3A-A9J0 TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A545 
       24.43        10.98         7.66         3.12        17.00        12.66 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FB-AAQ0 
        0.03        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-HV-A5A3 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8X 
       15.78        22.06         4.21        66.94         8.28        17.49 
TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8636 
       21.73        19.50         0.13         3.95         9.83        17.92 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A9TJ TCGA-IB-7644 
       10.13         6.38        21.60         5.26        19.82        12.95 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-8127 
       23.80        15.65         4.04        15.81         3.85        17.16 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO 
       15.85        15.12        21.90        15.88         4.73         7.86 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-S4-A8RM 
        8.05        12.92        19.20         8.78        15.45        24.23 
TCGA-S4-A8RO TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
       17.26        16.80         0.39        12.03        16.37        31.27 
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        15.22        14.40        21.44        45.47        58.98 
TCGA-3A-A9I7 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR 
       43.50        60.95        90.12        68.52        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6880 
       32.81        36.26        34.09        75.12        71.74         9.50 
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        16.37        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-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OP TCGA-HV-AA8V 
       12.89        13.84         7.63         9.50        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
        0.92         7.76         0.26        27.62        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
       23.21        12.03        19.59        12.43        14.93         4.96 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7645 
       21.70        16.14        10.85         1.08         0.23        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7887 
        4.77        21.90        15.35        19.82        41.33         3.62 
TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
       43.79        19.66        21.30        15.98         2.47        12.00 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUP 
        7.20        20.88         1.35         8.22         0.26        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-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        9.14        12.46        10.29        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E 
        9.40         0.30        23.08        22.85        39.98        14.14 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T5 TCGA-YB-A89D TCGA-Z5-AAPL 
       18.67        13.81        12.99        23.67        11.51        15.35 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.23 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             66.94              90.12 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             15.09              15.27 
[1] "0.0 - 66.9 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.6"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  17P LOSS MUTATED         0        2        2        15        56         2
  17P LOSS WILD-TYPE       1        3       13        15        65         3
                    vv
clus                 STAGE IV
  17P LOSS MUTATED          3
  17P LOSS WILD-TYPE        2
D70V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 2                  3
  STAGE IB                 2                 13
  STAGE IIA               15                 15
  STAGE IIB               56                 65
  STAGE III                2                  3
  STAGE IV                 3                  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  8 69  1
  17P LOSS WILD-TYPE  5 16 78  3
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                2                  5
  T2                8                 16
  T3               69                 78
  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"
D70V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   20 59
  17P LOSS WILD-TYPE 30 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     20   59
  17P LOSS WILD-TYPE   30   70
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               20                 30
  1               59                 70
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   33  3
  17P LOSS WILD-TYPE 52  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     33    3
  17P LOSS WILD-TYPE   52    2
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               33                 52
  1                3                  2
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   34 46
  17P LOSS WILD-TYPE 49 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     34   46
  17P LOSS WILD-TYPE   49   55
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               34                 49
  MALE                 46                 55
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   53 19
  17P LOSS WILD-TYPE 69 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     53   19
  17P LOSS WILD-TYPE   69   23
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                53                 69
  YES               19                 23
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17P LOSS MUTATED                                    71
  17P LOSS WILD-TYPE                                  82
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17P LOSS MUTATED                                       8
  17P LOSS WILD-TYPE                                    17
                    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
D70V9, multiclass
                                                  clus
vv                                                 17P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            71
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 17P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              82
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  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"
D70V10, continuous
D70V11, continuous
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   41 30  2  2
  17P LOSS WILD-TYPE 70 23  3  2
D70V12, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               41                 70
  R1               30                 23
  R2                2                  3
  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"
D70V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       5                         2    72
  17P LOSS WILD-TYPE     6                         5    89
D70V14, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    5                  6
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   72                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V15, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    2 57
  17P LOSS WILD-TYPE  3 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2   57
  17P LOSS WILD-TYPE    3   79
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               57                 79
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   12 10
  17Q LOSS WILD-TYPE 74 86
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                160 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                10                 86 
$`17Q LOSS MUTATED`
TCGA-2J-AABK TCGA-2J-AABP TCGA-2L-AAQL TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-AAPP 
       15.91        15.22         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-XN-A8T3 TCGA-YH-A8SY TCGA-YY-A8LH 
        8.05        31.27        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        42.31        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        58.98        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        33.57        60.95        90.12        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 
       24.43        75.12        71.74         9.50        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        12.66        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       22.06         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
       32.15        30.25        17.49         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        19.59         3.95         9.83        12.43        14.93 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
        4.96        21.70        16.14        10.13         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        1.08         0.23        19.82        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7887 
       21.90        15.35        19.82        15.65        41.33         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-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
       17.16        12.00         7.20        15.12        20.88         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-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 
       24.23        17.26        23.08        22.85        39.98        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-XN-A8T5 TCGA-YB-A89D TCGA-Z5-AAPL 
       16.37        23.67        11.51        15.35 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              2.01               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             66.28              90.12 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             15.88              14.70 
[1] "2.0 - 66.3 (15.9)" "0.0 - 90.1 (14.7)"
[1] "hr=" "1.2"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  17Q LOSS MUTATED         0        0        1         4        15         1
  17Q LOSS WILD-TYPE       1        5       14        26       106         4
                    vv
clus                 STAGE IV
  17Q LOSS MUTATED          1
  17Q LOSS WILD-TYPE        4
D71V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 1                 14
  STAGE IIA                4                 26
  STAGE IIB               15                106
  STAGE III                1                  4
  STAGE IV                 1                  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 LOSS MUTATED     0   1  21   0
  17Q LOSS WILD-TYPE   7  23 126   4
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                  7
  T2                1                 23
  T3               21                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"
D71V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     6  16
  17Q LOSS WILD-TYPE  44 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      6   16
  17Q LOSS WILD-TYPE   44  113
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                6                 44
  1               16                113
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   12  1
  17Q LOSS WILD-TYPE 73  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     12    1
  17Q LOSS WILD-TYPE   73    4
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               12                 73
  1                1                  4
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    6 16
  17Q LOSS WILD-TYPE 77 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      6   16
  17Q LOSS WILD-TYPE   77   85
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                6                 77
  MALE                 16                 85
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    14   6
  17Q LOSS WILD-TYPE 108  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     14    6
  17Q LOSS WILD-TYPE  108   36
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                14                108
  YES                6                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17Q LOSS MUTATED                                    17
  17Q LOSS WILD-TYPE                                 136
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17Q LOSS MUTATED                                       3
  17Q LOSS WILD-TYPE                                    22
                    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
D71V9, multiclass
                                                  clus
vv                                                 17Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            17
  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                             136
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            22
  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"
D71V10, continuous
D71V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED     8  10   0   2
  17Q LOSS WILD-TYPE 103  43   5   2
D71V12, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                8                103
  R1               10                 43
  R2                0                  5
  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"
D71V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       1                         1    20
  17Q LOSS WILD-TYPE    10                         6   141
D71V14, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   20                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"
D71V15, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  15
  17Q LOSS WILD-TYPE   4 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   15
  17Q LOSS WILD-TYPE    4  121
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               15                121
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   29 25
  18P LOSS WILD-TYPE 57 71
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                54                128 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                25                 71 
$`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        43.50         7.36        33.57 
TCGA-3A-A9IU TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
       15.06        24.43        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 
       16.37         0.03        11.61        37.15         8.02        15.78 
TCGA-H6-A45N TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8315 
       13.84         9.50         8.28        17.03        23.21         9.83 
TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A9TJ 
       21.70         6.38        21.60        10.85         1.08        19.82 
TCGA-IB-7644 TCGA-IB-7647 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7890 
       12.95        21.90        41.33         4.04        15.81        19.66 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A6UF 
        2.47        12.00        15.85         7.20        15.12        21.90 
TCGA-IB-AAUM TCGA-IB-AAUP TCGA-IB-AAUU TCGA-M8-A5N4 TCGA-OE-A75W TCGA-RB-AA9M 
        0.26        14.17         8.05        19.20         8.78         9.40 
TCGA-S4-A8RM TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YH-A8SY 
       24.23         0.39        13.81        12.03        31.27        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        42.31        31.86        14.47        15.22 
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        58.98        20.84        24.26        60.95 
TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV 
       90.12        68.52        63.85        50.70        32.81        36.26 
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         9.50        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        12.66        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 
       17.79        12.89        22.06         4.21         7.63        66.94 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
       32.15        30.25        17.49        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 
       19.59         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        39.98        16.80 
TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D 
       14.14        18.67        12.99        16.37        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.03               0.13 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             71.74              90.12 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            14.005             15.400 
[1] "0.0 - 71.7 (14.0)" "0.1 - 90.1 (15.4)"
[1] "hr=" "1"  
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  18P LOSS MUTATED         0        2        4        10        33         3
  18P LOSS WILD-TYPE       1        3       11        20        88         2
                    vv
clus                 STAGE IV
  18P LOSS MUTATED          3
  18P LOSS WILD-TYPE        2
D72V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 2                  3
  STAGE IB                 4                 11
  STAGE IIA               10                 20
  STAGE IIB               33                 88
  STAGE III                3                  2
  STAGE IV                 3                  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   6  44   2
  18P LOSS WILD-TYPE   4  18 103   2
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                3                  4
  T2                6                 18
  T3               44                103
  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"
D72V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   16 38
  18P LOSS WILD-TYPE 34 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16   38
  18P LOSS WILD-TYPE   34   91
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               16                 34
  1               38                 91
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   27  3
  18P LOSS WILD-TYPE 58  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     27    3
  18P LOSS WILD-TYPE   58    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               27                 58
  1                3                  2
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   21 34
  18P LOSS WILD-TYPE 62 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     21   34
  18P LOSS WILD-TYPE   62   67
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               21                 62
  MALE                 34                 67
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   36 11
  18P LOSS WILD-TYPE 86 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     36   11
  18P LOSS WILD-TYPE   86   31
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                36                 86
  YES               11                 31
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18P LOSS MUTATED                                    48
  18P LOSS WILD-TYPE                                 105
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18P LOSS MUTATED                                       5
  18P LOSS WILD-TYPE                                    20
                    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
D72V9, multiclass
                                                  clus
vv                                                 18P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            48
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 18P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             105
  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"
D72V10, continuous
D72V11, continuous
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   31 18  1  1
  18P LOSS WILD-TYPE 80 35  4  3
D72V12, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               31                 80
  R1               18                 35
  R2                1                  4
  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"
D72V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       3                         2    48
  18P LOSS WILD-TYPE     8                         5   113
D72V14, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    3                  8
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   48                113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    3 41
  18P LOSS WILD-TYPE  2 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   41
  18P LOSS WILD-TYPE    2   95
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               41                 95
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   45 59
  18Q LOSS WILD-TYPE 41 37
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               104                 78 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                59                 37 
$`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        42.31 
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 
       43.50        20.84         7.36        33.57        15.06        24.43 
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 
       12.66        16.37        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-HV-A5A3 TCGA-HV-A5A4 
       17.79        12.89        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7919 
        9.50        66.94         8.28        32.15        17.49        19.50 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49G 
       20.19        17.03        23.21         9.83        17.92        21.70 
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-A9TJ TCGA-IB-7644 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
       19.82        12.95        21.90        15.35        23.80        41.33 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       15.81        19.66         3.85         2.47        17.16        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        15.12        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX 
        0.26         4.73        14.17         8.05         9.14        12.92 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-S4-A8RM 
       19.20         8.78        15.45         3.12         9.40        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XD-AAUL 
       17.26        23.08         0.39        13.81        12.03        16.37 
TCGA-XN-A8T3 TCGA-YH-A8SY 
       31.27        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        15.22        45.47        58.98 
TCGA-3A-A9IC TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR 
       24.26        60.95        90.12        68.52        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6880 
       32.81        36.26        34.09        10.13        75.12         9.50 
TCGA-F2-7273 TCGA-F2-7276 TCGA-FB-A4P5 TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS 
       19.46         7.10         5.88         0.03        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-HV-AA8V TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       30.25        21.73         0.92         7.76         0.13         0.26 
TCGA-HZ-7924 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 
       27.62        12.03        19.59         3.95        12.43        14.93 
TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7651 
        4.96        16.14         0.23        49.38         4.77        19.82 
TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7891 TCGA-IB-7897 
       15.65         4.04         3.62        43.79        21.30        15.98 
TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
       20.88        15.88         7.86         6.02        11.11         7.40 
TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        9.44        13.28         7.56        12.46        10.29        13.68 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       15.32         0.30        22.85        39.98        16.80        14.14 
TCGA-US-A77J TCGA-XD-AAUH TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       18.67        12.99        23.67        11.51        66.28        15.35 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.26               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             71.74              90.12 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             15.09              15.27 
[1] "0.3 - 71.7 (15.1)" "0.0 - 90.1 (15.3)"
[1] "hr=" "1.4"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  18Q LOSS MUTATED         0        2        6        23        65         5
  18Q LOSS WILD-TYPE       1        3        9         7        56         0
                    vv
clus                 STAGE IV
  18Q LOSS MUTATED          5
  18Q LOSS WILD-TYPE        0
D73V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 2                  3
  STAGE IB                 6                  9
  STAGE IIA               23                  7
  STAGE IIB               65                 56
  STAGE III                5                  0
  STAGE IV                 5                  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 11 88  4
  18Q LOSS WILD-TYPE  4 13 59  0
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                3                  4
  T2               11                 13
  T3               88                 59
  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"
D73V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   31 73
  18Q LOSS WILD-TYPE 19 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     31   73
  18Q LOSS WILD-TYPE   19   56
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               31                 19
  1               73                 56
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   52  5
  18Q LOSS WILD-TYPE 33  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     52    5
  18Q LOSS WILD-TYPE   33    0
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               52                 33
  1                5                  0
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   44 62
  18Q LOSS WILD-TYPE 39 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     44   62
  18Q LOSS WILD-TYPE   39   39
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               44                 39
  MALE                 62                 39
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   71 24
  18Q LOSS WILD-TYPE 51 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     71   24
  18Q LOSS WILD-TYPE   51   18
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                71                 51
  YES               24                 18
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18Q LOSS MUTATED                                    93
  18Q LOSS WILD-TYPE                                  60
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18Q LOSS MUTATED                                      11
  18Q LOSS WILD-TYPE                                    14
                    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
D73V9, multiclass
                                                  clus
vv                                                 18Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            93
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          11
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 18Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              60
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            14
  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"
D73V10, continuous
D73V11, continuous
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED   57 35  3  3
  18Q LOSS WILD-TYPE 54 18  2  1
D73V12, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               57                 54
  R1               35                 18
  R2                3                  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"
D73V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED      10                         3    90
  18Q LOSS WILD-TYPE     1                         4    71
D73V14, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                   10                  1
  BLACK OR AFRICAN AMERICAN                3                  4
  WHITE                                   90                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    3 69
  18Q LOSS WILD-TYPE  2 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   69
  18Q LOSS WILD-TYPE    2   67
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               69                 67
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    9 10
  19P LOSS WILD-TYPE 77 86
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                163 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                10                 86 
$`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        15.22        15.06        24.43        15.95 
TCGA-H6-8124 TCGA-HV-A5A6 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-HZ-8636 TCGA-IB-7646 
       12.89        66.94         0.13         3.95        17.92         4.77 
TCGA-IB-7885 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-L1-A7W4 TCGA-LB-A7SX 
       41.33        21.90         1.35         8.22         9.14        12.92 
TCGA-XN-A8T3 
       31.27 

$`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        42.31        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        58.98        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        33.57        60.95        90.12        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY 
       50.70        32.81        36.26        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         9.50        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        12.66        16.37 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY 
        0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
       17.79        13.84        22.06         4.21         7.63         9.50 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 
        8.28        32.15        30.25        17.49        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-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        12.95 
TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
       49.38        21.90        15.35        19.82        23.80        15.65 
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-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-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
        8.05        13.28         7.56        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        16.37        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.13               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             66.94              90.12 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             15.06              15.32 
[1] "0.1 - 66.9 (15.1)" "0.0 - 90.1 (15.3)"
[1] "hr=" "1"  
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  19P LOSS MUTATED         0        0        1         1        16         0
  19P LOSS WILD-TYPE       1        5       14        29       105         5
                    vv
clus                 STAGE IV
  19P LOSS MUTATED          1
  19P LOSS WILD-TYPE        4
D74V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 1                 14
  STAGE IIA                1                 29
  STAGE IIB               16                105
  STAGE III                0                  5
  STAGE IV                 1                  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 LOSS MUTATED     0   1  18   0
  19P LOSS WILD-TYPE   7  23 129   4
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                0                  7
  T2                1                 23
  T3               18                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"
D74V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3  16
  19P LOSS WILD-TYPE  47 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3   16
  19P LOSS WILD-TYPE   47  113
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                3                 47
  1               16                113
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   11  1
  19P LOSS WILD-TYPE 74  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     11    1
  19P LOSS WILD-TYPE   74    4
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               11                 74
  1                1                  4
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    9 10
  19P LOSS WILD-TYPE 74 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9   10
  19P LOSS WILD-TYPE   74   91
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                9                 74
  MALE                 10                 91
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    12   5
  19P LOSS WILD-TYPE 110  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     12    5
  19P LOSS WILD-TYPE  110   37
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                12                110
  YES                5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19P LOSS MUTATED                                    17
  19P LOSS WILD-TYPE                                 136
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19P LOSS MUTATED                                       1
  19P LOSS WILD-TYPE                                    24
                    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
D74V9, multiclass
                                                  clus
vv                                                 19P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            17
  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                             136
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            24
  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"
D74V10, continuous
D74V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    11   7   1   0
  19P LOSS WILD-TYPE 100  46   4   4
D74V12, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               11                100
  R1                7                 46
  R2                1                  4
  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"
D74V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         1    17
  19P LOSS WILD-TYPE    10                         6   144
D74V14, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                 10
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   17                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"
D74V15, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  14
  19P LOSS WILD-TYPE   4 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   14
  19P LOSS WILD-TYPE    4  122
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               14                122
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    5  7
  19Q LOSS WILD-TYPE 81 89
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                170 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                 89 
$`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 TCGA-XN-A8T3 
       17.92         4.77        41.33         8.22         9.14        31.27 

$`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        42.31        15.91        15.22        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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN 
        7.36        24.26        33.57        60.95        90.12        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 
       10.13        24.43        75.12        71.74        10.98         9.50 
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        12.66        16.37         0.03        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-HV-A5A3 
       20.35        15.78        17.79        13.84        22.06         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
        7.63         9.50        66.94         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 
       17.49        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-8638 TCGA-HZ-A49G 
       19.59         9.83        12.43        14.93         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 
        1.08         0.23        19.82        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-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         1.35        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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
       39.98        16.80        14.14         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        16.37        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              3.95               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             41.33              90.12 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             15.21              15.17 
[1] "4.0 - 41.3 (15.2)" "0.0 - 90.1 (15.2)"
[1] "hr=" "1"  
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  19Q LOSS MUTATED         0        0        1         1         9         0
  19Q LOSS WILD-TYPE       1        5       14        29       112         5
                    vv
clus                 STAGE IV
  19Q LOSS MUTATED          1
  19Q LOSS WILD-TYPE        4
D75V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 1                 14
  STAGE IIA                1                 29
  STAGE IIB                9                112
  STAGE III                0                  5
  STAGE IV                 1                  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 LOSS MUTATED     0   1  11   0
  19Q LOSS WILD-TYPE   7  23 136   4
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                0                  7
  T2                1                 23
  T3               11                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"
D75V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     3   9
  19Q LOSS WILD-TYPE  47 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    9
  19Q LOSS WILD-TYPE   47  120
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                3                 47
  1                9                120
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    7  1
  19Q LOSS WILD-TYPE 78  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      7    1
  19Q LOSS WILD-TYPE   78    4
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                7                 78
  1                1                  4
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    5  7
  19Q LOSS WILD-TYPE 78 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5    7
  19Q LOSS WILD-TYPE   78   94
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                5                 78
  MALE                  7                 94
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     6   5
  19Q LOSS WILD-TYPE 116  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    5
  19Q LOSS WILD-TYPE  116   37
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 6                116
  YES                5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19Q LOSS MUTATED                                    11
  19Q LOSS WILD-TYPE                                 142
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19Q LOSS MUTATED                                       1
  19Q LOSS WILD-TYPE                                    24
                    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
D75V9, multiclass
                                                  clus
vv                                                 19Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  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                             142
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            24
  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"
D75V10, continuous
D75V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED     7   4   1   0
  19Q LOSS WILD-TYPE 104  49   4   4
D75V12, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                7                104
  R1                4                 49
  R2                1                  4
  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"
D75V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0    12
  19Q LOSS WILD-TYPE    11                         7   149
D75V14, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   12                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"
D75V15, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1   9
  19Q LOSS WILD-TYPE   4 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    9
  19Q LOSS WILD-TYPE    4  127
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                9                127
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED   10  9
  20P LOSS WILD-TYPE 76 87
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                163 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 87 
$`20P LOSS MUTATED`
TCGA-2J-AABH TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9IB TCGA-3A-A9IC TCGA-FB-A78T 
       42.31        22.49        12.95         7.36        24.26         0.03 
TCGA-FB-AAQ1 TCGA-FZ-5920 TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A9TJ 
        4.04         2.01        21.70        10.13        21.60        19.82 
TCGA-IB-7887 TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUU TCGA-LB-A7SX TCGA-M8-A5N4 
        3.62        21.90        15.88         8.05        12.92        19.20 
TCGA-XN-A8T3 
       31.27 

$`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        15.22 
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        58.98        43.50        20.84        33.57 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        90.12        68.52        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       71.74        10.98         9.50        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        12.66        16.37 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       13.84        22.06         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7918 
        8.28        32.15        30.25        17.49        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        19.59         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A4BH 
       12.43        14.93        17.92         4.96        16.14         6.38 
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-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       41.33         4.04        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-A6UG TCGA-IB-A7LX TCGA-IB-AAUM 
        7.20        15.12        20.88         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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        16.37        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.03               0.13 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             42.31              90.12 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             15.88              15.12 
[1] "0.0 - 42.3 (15.9)" "0.1 - 90.1 (15.1)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  20P LOSS MUTATED         0        0        1         2        15         1
  20P LOSS WILD-TYPE       1        5       14        28       106         4
                    vv
clus                 STAGE IV
  20P LOSS MUTATED          1
  20P LOSS WILD-TYPE        4
D76V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 1                 14
  STAGE IIA                2                 28
  STAGE IIB               15                106
  STAGE III                1                  4
  STAGE IV                 1                  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   2  17   1
  20P LOSS WILD-TYPE   7  22 130   3
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                0                  7
  T2                2                 22
  T3               17                130
  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"
D76V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     5  15
  20P LOSS WILD-TYPE  45 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5   15
  20P LOSS WILD-TYPE   45  114
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                5                 45
  1               15                114
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    9  1
  20P LOSS WILD-TYPE 76  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9    1
  20P LOSS WILD-TYPE   76    4
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                9                 76
  1                1                  4
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    8 12
  20P LOSS WILD-TYPE 75 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   12
  20P LOSS WILD-TYPE   75   89
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                 75
  MALE                 12                 89
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12   6
  20P LOSS WILD-TYPE 110  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12    6
  20P LOSS WILD-TYPE  110   36
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                12                110
  YES                6                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20P LOSS MUTATED                                    17
  20P LOSS WILD-TYPE                                 136
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20P LOSS MUTATED                                       3
  20P LOSS WILD-TYPE                                    22
                    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
D76V9, multiclass
                                                  clus
vv                                                 20P 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                                                 20P LOSS 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"
D76V10, continuous
D76V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    10  10   0   0
  20P LOSS WILD-TYPE 101  43   5   4
D76V12, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               10                101
  R1               10                 43
  R2                0                  5
  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"
D76V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         2    17
  20P LOSS WILD-TYPE    11                         5   144
D76V14, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   17                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"
D76V15, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  15
  20P LOSS WILD-TYPE   4 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   15
  20P LOSS WILD-TYPE    4  121
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               15                121
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    1  3
  20Q LOSS WILD-TYPE 85 93
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                178 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 93 
$`20Q LOSS MUTATED`
TCGA-2L-AAQE TCGA-HZ-A49I TCGA-LB-A7SX TCGA-XN-A8T3 
       22.49        10.13        12.92        31.27 

$`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        42.31        31.86        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.22        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
       20.84         7.36        24.26        33.57        60.95        90.12 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       68.52        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.50        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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
       12.89        13.84        22.06         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 
       66.94         8.28        32.15        30.25        17.49        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        19.59         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-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       16.14         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        16.37        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             10.13               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             31.27              90.12 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            17.705             15.170 
[1] "10.1 - 31.3 (17.7)" "0.0 - 90.1 (15.2)" 
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  20Q LOSS MUTATED         0        0        1         0         4         0
  20Q LOSS WILD-TYPE       1        5       14        30       117         5
                    vv
clus                 STAGE IV
  20Q LOSS MUTATED          0
  20Q LOSS WILD-TYPE        5
D77V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 1                 14
  STAGE IIA                0                 30
  STAGE IIB                4                117
  STAGE III                0                  5
  STAGE IV                 0                  5
[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   1   4   0
  20Q LOSS WILD-TYPE   7  23 143   4
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                0                  7
  T2                1                 23
  T3                4                143
  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
  20Q LOSS MUTATED     1   4
  20Q LOSS WILD-TYPE  49 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    4
  20Q LOSS WILD-TYPE   49  125
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                1                 49
  1                4                125
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  0
  20Q LOSS WILD-TYPE 83  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    0
  20Q LOSS WILD-TYPE   83    5
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                2                 83
  1                0                  5
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  4
  20Q LOSS WILD-TYPE 82 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    4
  20Q LOSS WILD-TYPE   82   97
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 82
  MALE                  4                 97
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   2
  20Q LOSS WILD-TYPE 120  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    2
  20Q LOSS WILD-TYPE  120   40
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 2                120
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20Q LOSS MUTATED                                     5
  20Q LOSS WILD-TYPE                                 148
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                    25
                    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
D77V9, multiclass
                                                  clus
vv                                                 20Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  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                             148
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            25
  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"
D77V10, continuous
D77V11, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 44 
        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-XN-A8T5         TCGA-YY-A8LH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     2   3   0   0
  20Q LOSS WILD-TYPE 109  50   5   4
D77V12, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                2                109
  R1                3                 50
  R2                0                  5
  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"
D77V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         1     4
  20Q LOSS WILD-TYPE    11                         6   157
D77V14, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                 11
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    4                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   3
  20Q LOSS WILD-TYPE   4 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    3
  20Q LOSS WILD-TYPE    4  133
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                3                133
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   28 29
  21Q LOSS WILD-TYPE 58 67
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                57                125 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                 67 
$`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        15.22        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        32.81        10.13        24.43 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPY 
        3.12        17.00        12.66         0.03        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-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OP TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 
        9.50        66.94        32.15         0.92        19.50         0.13 
TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q 
        3.95        17.92         6.38        21.60         5.26         1.08 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 
       19.82        12.95         4.77        15.35        19.82        41.33 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A6UG 
        4.04         3.62        15.85        15.12        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUU TCGA-OE-A75W TCGA-US-A77G 
        8.22         7.86        14.17         8.05         8.78         0.39 
TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YY-A8LH 
       31.27        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        42.31        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        58.98        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       24.26        33.57        60.95        90.12        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        36.26        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         9.50        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        16.37        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-HV-A5A3 TCGA-HV-A5A4 
       36.20        20.35        17.79        13.84         4.21         7.63 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7920 TCGA-HZ-7923 
        8.28        30.25        17.49        21.73         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        19.59 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93         4.96        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7652 
       10.13        10.85         0.23        49.38        21.90        23.80 
TCGA-IB-7654 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 
       15.65        43.79        15.81        19.66        21.30         3.85 
TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST 
       15.98         2.47        17.16        12.00         7.20        20.88 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
       15.88         0.26         4.73         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-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-S4-A8RP TCGA-US-A774 
        9.40         0.30        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.03        16.37        23.67        12.76        15.35 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.03               0.23 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             66.94              90.12 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             14.17              15.45 
[1] "0.0 - 66.9 (14.2)" "0.2 - 90.1 (15.4)"
[1] "hr=" "1.2"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  21Q LOSS MUTATED         0        0        2         7        46         0
  21Q LOSS WILD-TYPE       1        5       13        23        75         5
                    vv
clus                 STAGE IV
  21Q LOSS MUTATED          3
  21Q LOSS WILD-TYPE        2
D78V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA                7                 23
  STAGE IIB               46                 75
  STAGE III                0                  5
  STAGE IV                 3                  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  4 54  0
  21Q LOSS WILD-TYPE  7 20 93  4
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                0                  7
  T2                4                 20
  T3               54                 93
  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"
D78V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   10 48
  21Q LOSS WILD-TYPE 40 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     10   48
  21Q LOSS WILD-TYPE   40   81
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               10                 40
  1               48                 81
[1] 2 2
[1] FALSE
D78V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   34  3
  21Q LOSS WILD-TYPE 51  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     34    3
  21Q LOSS WILD-TYPE   51    2
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               34                 51
  1                3                  2
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   22 36
  21Q LOSS WILD-TYPE 61 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     22   36
  21Q LOSS WILD-TYPE   61   65
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               22                 61
  MALE                 36                 65
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   35 14
  21Q LOSS WILD-TYPE 87 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     35   14
  21Q LOSS WILD-TYPE   87   28
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                35                 87
  YES               14                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  21Q LOSS MUTATED                                    50
  21Q LOSS WILD-TYPE                                 103
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  21Q LOSS MUTATED                                       7
  21Q LOSS WILD-TYPE                                    18
                    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
D78V9, multiclass
                                                  clus
vv                                                 21Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            50
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 21Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             103
  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"
D78V10, continuous
D78V11, continuous
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   33 21  0  1
  21Q LOSS WILD-TYPE 78 32  5  3
D78V12, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               33                 78
  R1               21                 32
  R2                0                  5
  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"
D78V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       3                         1    52
  21Q LOSS WILD-TYPE     8                         6   109
D78V14, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    3                  8
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   52                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3 39
  21Q LOSS WILD-TYPE  2 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3   39
  21Q LOSS WILD-TYPE    2   97
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               39                 97
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   26 20
  22Q LOSS WILD-TYPE 60 76
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                46                136 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                20                 76 
$`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        42.31        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        90.12        15.06        10.98 
TCGA-F2-A44H TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       19.27         0.03        11.61        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5924 TCGA-HV-A5A5 TCGA-HV-A7OL 
        5.03        24.36         2.01        15.78         9.50         8.28 
TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A8P1 
       17.92         6.38        21.60         5.26         1.08         0.23 
TCGA-IB-7646 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A7LX 
        4.77         4.04        17.16        15.85        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUU TCGA-OE-A75W TCGA-PZ-A5RE TCGA-RB-AA9M 
       15.88         7.86         8.05         8.78        15.45         9.40 
TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YY-A8LH 
       16.37        31.27        11.51        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        15.22        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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR 
        7.36        33.57        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 
       32.81        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A7TX 
       71.74         9.50        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        12.66        16.37        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
        4.21         7.63        66.94        32.15        30.25        17.49 
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        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       16.14        10.13        10.85        19.82        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-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-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
       15.98         2.47        12.00         7.20        15.12        20.88 
TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        1.35         0.26         4.73        14.17         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-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29        19.20        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T5 TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.03        23.67        12.76        15.35 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.03               0.13 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             90.12              75.12 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            14.765             15.270 
[1] "0.0 - 90.1 (14.8)" "0.1 - 75.1 (15.3)"
[1] "hr=" "1.2"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  22Q LOSS MUTATED         1        0        2        10        32         0
  22Q LOSS WILD-TYPE       0        5       13        20        89         5
                    vv
clus                 STAGE IV
  22Q LOSS MUTATED          1
  22Q LOSS WILD-TYPE        4
D79V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  5
  STAGE IB                 2                 13
  STAGE IIA               10                 20
  STAGE IIB               32                 89
  STAGE III                0                  5
  STAGE IV                 1                  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 LOSS MUTATED     2   4  40   0
  22Q LOSS WILD-TYPE   5  20 107   4
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                2                  5
  T2                4                 20
  T3               40                107
  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
  22Q LOSS MUTATED   11 33
  22Q LOSS WILD-TYPE 39 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     11   33
  22Q LOSS WILD-TYPE   39   96
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               11                 39
  1               33                 96
[1] 2 2
[1] FALSE
D79V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   23  1
  22Q LOSS WILD-TYPE 62  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     23    1
  22Q LOSS WILD-TYPE   62    4
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               23                 62
  1                1                  4
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   14 32
  22Q LOSS WILD-TYPE 69 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     14   32
  22Q LOSS WILD-TYPE   69   69
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               14                 69
  MALE                 32                 69
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   27 12
  22Q LOSS WILD-TYPE 95 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     27   12
  22Q LOSS WILD-TYPE   95   30
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                27                 95
  YES               12                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  22Q LOSS MUTATED                                    38
  22Q LOSS WILD-TYPE                                 115
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  22Q LOSS MUTATED                                       7
  22Q LOSS WILD-TYPE                                    18
                    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
D79V9, multiclass
                                                  clus
vv                                                 22Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            38
  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                             115
  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"
D79V10, continuous
D79V11, continuous
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   27 15  1  0
  22Q LOSS WILD-TYPE 84 38  4  4
D79V12, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               27                 84
  R1               15                 38
  R2                1                  4
  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"
D79V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       3                         1    42
  22Q LOSS WILD-TYPE     8                         6   119
D79V14, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    3                  8
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   42                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"
D79V15, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     1  32
  22Q LOSS WILD-TYPE   4 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   32
  22Q LOSS WILD-TYPE    4  104
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               32                104
[1] 2 2
[1] FALSE

Clustering(80) Variable = XP LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED   16 10
  XP LOSS WILD-TYPE 70 86
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               26               156 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               10                86 
$`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        33.57 
TCGA-3A-A9IL TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAQ0 TCGA-FZ-5924 TCGA-H6-8124 
       90.12        17.00         0.03        15.55        15.78        12.89 
TCGA-HV-A7OP TCGA-HZ-7918 TCGA-HZ-8001 TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       32.15         0.92        23.21         0.23        19.82        23.80 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUN TCGA-OE-A75W TCGA-Q3-AA2A TCGA-S4-A8RO 
        1.35         8.22         4.73         8.78         3.12        17.26 
TCGA-US-A774 TCGA-YY-A8LH 
       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        42.31        15.91        14.47        15.22        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        58.98        43.50         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        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.50        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        12.66        16.37        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-HV-A5A3 TCGA-HV-A5A4 
       20.35        17.79        13.84        22.06         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7289 
        9.50        66.94         8.28        30.25        17.49        21.73 
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        19.59         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-IB-7644 
        6.38        21.60         5.26        10.85         1.08        12.95 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 
       49.38         4.77        21.90        15.35        19.82        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-A7M4 
       15.85         7.20        15.12        20.88        21.90        15.88 
TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         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-PZ-A5RE TCGA-Q3-A5QY TCGA-RB-A7B8 
       12.46        10.29        19.20        15.45        13.68        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 
        9.40         0.30        24.23        23.08        39.98        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       16.37        31.27        23.67        11.51        12.76        15.35 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.03              0.13 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            90.12             75.12 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            17.13             14.70 
[1] "0.0 - 90.1 (17.1)" "0.1 - 75.1 (14.7)"
[1] "hr=" "1.7"
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  XP LOSS MUTATED         1        1        3         6        14         1
  XP LOSS WILD-TYPE       0        4       12        24       107         4
                   vv
clus                STAGE IV
  XP LOSS MUTATED          1
  XP LOSS WILD-TYPE        4
D80V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                1                 4
  STAGE IB                3                12
  STAGE IIA               6                24
  STAGE IIB              14               107
  STAGE III               1                 4
  STAGE IV                1                 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  21   1
  XP LOSS WILD-TYPE   5  21 126   3
D80V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               2                 5
  T2               3                21
  T3              21               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"
D80V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    10  16
  XP LOSS WILD-TYPE  40 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     10   16
  XP LOSS WILD-TYPE   40  113
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              10                40
  1              16               113
[1] 2 2
[1] FALSE
D80V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   14  1
  XP LOSS WILD-TYPE 71  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     14    1
  XP LOSS WILD-TYPE   71    4
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              14                71
  1               1                 4
[1] 2 2
[1] FALSE
D80V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   12 15
  XP LOSS WILD-TYPE 71 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     12   15
  XP LOSS WILD-TYPE   71   86
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              12                71
  MALE                15                86
[1] 2 2
[1] FALSE
D80V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    16   7
  XP LOSS WILD-TYPE 106  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     16    7
  XP LOSS WILD-TYPE  106   35
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               16               106
  YES               7                35
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XP LOSS MUTATED                                    22
  XP LOSS WILD-TYPE                                 131
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XP LOSS MUTATED                                       5
  XP LOSS WILD-TYPE                                    20
                   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
D80V9, multiclass
                                                  clus
vv                                                 XP LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 XP LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            131
  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"
D80V10, continuous
D80V11, continuous
                   vv
clus                R0 R1 R2 RX
  XP LOSS MUTATED   21  5  0  1
  XP LOSS WILD-TYPE 90 48  5  3
D80V12, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              21                90
  R1               5                48
  R2               0                 5
  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"
D80V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       2                         0    25
  XP LOSS WILD-TYPE     9                         7   136
D80V14, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   2                 9
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  25               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"
D80V15, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     1  21
  XP LOSS WILD-TYPE   4 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1   21
  XP LOSS WILD-TYPE    4  115
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              21               115
[1] 2 2
[1] FALSE

Clustering(81) Variable = XQ LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   11  7
  XQ LOSS WILD-TYPE 75 89
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18               164 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                89 
$`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        33.57 
TCGA-3A-A9IL TCGA-F2-A8YN TCGA-FZ-5924 TCGA-H6-8124 TCGA-HV-A7OP TCGA-HZ-7918 
       90.12        17.00        15.78        12.89        32.15         0.92 
TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-A6UG TCGA-IB-AAUN TCGA-OE-A75W TCGA-US-A776 
        0.23        23.80         1.35         4.73         8.78        39.98 

$`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        42.31        15.91        14.47        15.22        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        58.98        43.50         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        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        75.12        71.74        10.98 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
        9.50        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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 
       17.49        21.73        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        19.59 
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-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08        19.82        12.95        49.38         4.77 
TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7654 TCGA-IB-7885 TCGA-IB-7886 
       21.90        15.35        19.82        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-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.12        20.88        21.90         8.22        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-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-S4-A8RP TCGA-US-A774 
        9.40         0.30        24.23        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.23              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            90.12             75.12 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           18.920            14.995 
[1] "0.2 - 90.1 (18.9)" "0.0 - 75.1 (15.0)"
[1] "hr=" "1.7"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  XQ LOSS MUTATED         1        1        2         6         8         0
  XQ LOSS WILD-TYPE       0        4       13        24       113         5
                   vv
clus                STAGE IV
  XQ LOSS MUTATED          0
  XQ LOSS WILD-TYPE        5
D81V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                1                 4
  STAGE IB                2                13
  STAGE IIA               6                24
  STAGE IIB               8               113
  STAGE III               0                 5
  STAGE IV                0                 5
[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  13   0
  XQ LOSS WILD-TYPE   5  21 134   4
D81V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               2                 5
  T2               3                21
  T3              13               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"
D81V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     8   9
  XQ LOSS WILD-TYPE  42 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8    9
  XQ LOSS WILD-TYPE   42  120
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               8                42
  1               9               120
[1] 2 2
[1] FALSE
D81V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   13  0
  XQ LOSS WILD-TYPE 72  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13    0
  XQ LOSS WILD-TYPE   72    5
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              13                72
  1               0                 5
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    6 12
  XQ LOSS WILD-TYPE 77 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6   12
  XQ LOSS WILD-TYPE   77   89
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               6                77
  MALE                12                89
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    11   5
  XQ LOSS WILD-TYPE 111  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11    5
  XQ LOSS WILD-TYPE  111   37
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               11               111
  YES               5                37
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XQ LOSS MUTATED                                    13
  XQ LOSS WILD-TYPE                                 140
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XQ LOSS MUTATED                                       4
  XQ LOSS WILD-TYPE                                    21
                   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
D81V9, multiclass
                                                  clus
vv                                                 XQ LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 XQ LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            140
  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"
D81V10, continuous
D81V11, continuous
                   vv
clus                R0 R1 R2 RX
  XQ LOSS MUTATED   14  4  0  0
  XQ LOSS WILD-TYPE 97 49  5  4
D81V12, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              14                97
  R1               4                49
  R2               0                 5
  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"
D81V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       2                         0    16
  XQ LOSS WILD-TYPE     9                         7   145
D81V14, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   2                 9
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  16               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"
D81V15, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  13
  XQ LOSS WILD-TYPE   5 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   13
  XQ LOSS WILD-TYPE    5  123
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              13               123
[1] 2 2
[1] FALSE
