[1] "ofn"        "-oTESCA-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/15078602/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/15084413/transformed.cor.cli.txt"

nPatients in clinical file=174, in cluster file=184, common to both=173
[1]  82 173
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               33               140 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               33               140 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               57               116 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               57               116 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               56               117 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               56               117 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               42               131 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               42               131 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               28               145 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               28               145 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               70               103 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               70               103 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               16               157 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               16               157 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               157 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               157 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               68               105 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               68               105 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               154 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               154 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               36               137 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               36               137 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               31               142 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               31               142 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              104                69 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              104                69 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               84                89 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               84                89 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               65               108 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               65               108 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               94                79 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               94                79 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               160 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               160 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               29               144 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               29               144 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                38                135 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                38                135 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                29                144 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                29                144 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                38                135 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                38                135 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                144 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                144 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                53                120 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                53                120 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                137 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                137 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                40                133 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                40                133 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                44                129 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                44                129 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                27                146 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                27                146 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                37                136 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                37                136 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                35                138 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                35                138 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                143 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                143 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                41                132 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                41                132 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                49                124 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                49                124 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                26                147 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                26                147 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                26                147 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                26                147 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                37                136 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                37                136 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               102                 71 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               102                 71 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               110                 63 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               110                 63 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                16                157 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                16                157 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                29                144 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                29                144 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               21               152 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               21               152 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               35               138 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               35               138 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               139 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               139 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               153 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               153 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               162 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               162 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               155 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               155 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               86                87 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               86                87 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               32               141 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               32               141 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               99                74 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               99                74 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               85                88 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               85                88 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               45               128 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               45               128 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               80                93 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               80                93 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               36               137 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               36               137 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               37               136 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               37               136 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               160 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               160 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               22               151 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               22               151 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               115 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               115 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               151 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               151 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               96                77 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               96                77 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               61               112 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               61               112 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                129 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                129 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                43                130 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                43                130 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                47                126 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                47                126 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                52                121 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                52                121 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                32                141 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                32                141 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                28                145 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                28                145 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                62                111 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                62                111 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                43                130 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                43                130 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                51                122 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                51                122 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                53                120 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                53                120 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                50                123 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                50                123 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                68                105 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                68                105 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                149 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                149 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                106 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                106 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                95                 78 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                95                 78 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                61                112 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                61                112 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                48                125 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                48                125 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                155 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                155 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                165 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                165 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                99                 74 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                99                 74 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                70                103 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                70                103 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               57               116 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               57               116 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39               134 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39               134 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATIONS_RADIATION_REGIMENINDICATION"
[12] "NUMBER_PACK_YEARS_SMOKED"              
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 173 columns.

[1] "Batch" "15"   
[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=69,	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=105,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              12-3-2015 26-3-2015
freq.values   "1"       "172"    
freq.contrast "172"     "1"      
both >= 3     "FALSE"   "FALSE"  
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 173 columns, 1 survival variables, and 9 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"           "NEOPLASM_DISEASESTAGE"   
[3] "PATHOLOGY_T_STAGE"        "PATHOLOGY_N_STAGE"       
[5] "PATHOLOGY_M_STAGE"        "GENDER"                  
[7] "NUMBER_PACK_YEARS_SMOKED" "RACE"                    
[9] "ETHNICITY"               
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
 1 30 36 85  5 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   31    36    85     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 30 36 85  5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   31    36    85     5 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
71 64 12  8 
[1] "table(vv)"
vv
N0 N1 N2 N3 
71 64 12  8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
71 64 12  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
71 64 12  8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=45, 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   18 14
  1P GAIN WILD-TYPE 82 57
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               32               139 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               14                57 
$`1P GAIN MUTATED`
TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A93E 
       13.94        20.09        17.03        23.41         4.67        25.22 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
       47.93        18.35         7.43         0.36         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        2.66        13.22        13.41        10.36         5.92        10.45 
TCGA-LN-A49X TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A9FO TCGA-R6-A6L4 TCGA-R6-A6XG 
        0.10        13.22        12.33         0.13        14.70        29.59 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-X8-AAAR 
       15.78        12.69         3.42        22.82         8.12        10.16 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

$`1P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30         0.53         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        19.99        21.01         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG 
        8.71         2.60        25.12         7.40        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        27.12        83.24        52.57        46.09 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.25        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
        5.06         7.04         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        1.45         7.00        20.02        20.38         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         4.44        18.81        19.96        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       46.19        15.06        11.24         9.17        15.91         3.42 
TCGA-Z6-AAPN 
        2.66 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              0.1               0.1 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            47.93            122.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            12.51             12.59 
[1] "0.1 - 47.9 (12.5)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.4"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         1        1        0        0         5         9
  1P GAIN WILD-TYPE       7        4        7        1        34        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           2          2          2          2        0
  1P GAIN WILD-TYPE        23         10          8          5        5
                   vv
clus                STAGE IVA
  1P GAIN MUTATED           2
  1P GAIN WILD-TYPE         2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 1                 4
  STAGE IB                 0                 7
  STAGE II                 0                 1
  STAGE IIA                5                34
  STAGE IIB                9                20
  STAGE III                2                23
  STAGE IIIA               2                10
  STAGE IIIB               2                 8
  STAGE IIIC               2                 5
  STAGE IV                 0                 5
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  1P GAIN MUTATED       8  6 15  0
  1P GAIN WILD-TYPE    23 30 70  5
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1               8                23
  T2                  6                30
  T3                 15                70
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  1P GAIN MUTATED   12 13  2  2
  1P GAIN WILD-TYPE 59 51 10  6
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              12                59
  N1              13                51
  N2               2                10
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    21   2
  1P GAIN WILD-TYPE 105   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     21    2
  1P GAIN WILD-TYPE  105    7
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              21               105
  1               2                 7
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     3  30
  1P GAIN WILD-TYPE  21 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3   30
  1P GAIN WILD-TYPE   21  119
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3                21
  MALE                30               119
[1] 2 2
[1] FALSE
D1V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       9                         1    22
  1P GAIN WILD-TYPE    32                         1    89
D1V9, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   9                32
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  22                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"
D1V10, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1 19
  1P GAIN WILD-TYPE  2 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   19
  1P GAIN WILD-TYPE    2   62
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              19                62
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   30 26
  1Q GAIN WILD-TYPE 70 45
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               56               115 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26                45 
$`1Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 
       13.94         8.94        20.09         0.85        20.12        18.64 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A93D 
       17.03         0.79        23.41        12.82         4.67        31.56 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       25.22         0.30         3.68        32.61        47.93        18.35 
TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        7.43         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L7-A6VZ 
        2.66        12.92        13.22         5.49        13.41        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 
        5.92        10.45        15.35         0.10         0.10        12.49 
TCGA-LN-A4A3 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HZ 
       12.76        13.22         4.47        12.33        12.00        13.18 
TCGA-LN-A9FO TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RC 
        0.13        14.70        29.59        15.78        12.69         3.42 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA4D TCGA-VR-AA7I TCGA-X8-AAAR 
       22.82         8.12        28.11        46.19        15.91        10.16 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

$`1Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       16.24         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A6QS 
       20.78         2.63         3.88         9.30         0.53         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J 
       23.18        24.03         6.28         3.16        30.25         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
        8.94        24.00         4.70        19.99        21.01         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NG 
        7.13         6.94         8.71         2.60        25.12        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.55         7.76        21.37         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N 
       27.12        83.24        52.57        46.09        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       13.41         0.10        13.15        13.25        12.46        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU 
       25.25        10.52        12.23        12.03        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.82         8.02         7.59         5.06         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
       53.95         9.30         2.89         1.45         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
       18.81        19.96        12.43         1.55        18.31        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       18.18        42.87        15.06        11.24         9.17         3.42 
TCGA-Z6-AAPN 
        2.66 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              0.1               0.1 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             55.5             122.1 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           12.725            12.460 
[1] "0.1 - 55.5 (12.7)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.5"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         2        1        2        0        11        12
  1Q GAIN WILD-TYPE       6        4        5        1        28        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           7          4          3          3        2
  1Q GAIN WILD-TYPE        18          8          7          4        3
                   vv
clus                STAGE IVA
  1Q GAIN MUTATED           3
  1Q GAIN WILD-TYPE         1
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 1                 4
  STAGE IB                 2                 5
  STAGE II                 0                 1
  STAGE IIA               11                28
  STAGE IIB               12                17
  STAGE III                7                18
  STAGE IIIA               4                 8
  STAGE IIIB               3                 7
  STAGE IIIC               3                 4
  STAGE IV                 2                 3
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  1Q GAIN MUTATED      14 11 26  2
  1Q GAIN WILD-TYPE    17 25 59  3
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              14                17
  T2                 11                25
  T3                 26                59
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  1Q GAIN MUTATED   22 25  3  3
  1Q GAIN WILD-TYPE 49 39  9  5
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              22                49
  N1              25                39
  N2               3                 9
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   41  5
  1Q GAIN WILD-TYPE 85  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     41    5
  1Q GAIN WILD-TYPE   85    4
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              41                85
  1               5                 4
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    4 53
  1Q GAIN WILD-TYPE 20 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4   53
  1Q GAIN WILD-TYPE   20   96
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               4                20
  MALE                53                96
[1] 2 2
[1] FALSE
D2V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED      17                         1    36
  1Q GAIN WILD-TYPE    24                         1    75
D2V9, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                  17                24
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  36                75
[1] 3 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, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    1 31
  1Q GAIN WILD-TYPE  2 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   31
  1Q GAIN WILD-TYPE    2   50
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              31                50
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   31 24
  2P GAIN WILD-TYPE 69 47
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               55               116 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               24                47 
$`2P GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RF TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A8O2 
       13.94         8.94         6.21        18.64        23.41         4.67 
TCGA-JY-A6FA TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
       44.75        25.22         4.31         3.68        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y 
       18.35         3.32         3.16         7.13         2.60         0.36 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S 
       52.57        10.36         5.92        10.45         0.10        13.15 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.76        12.59         0.10 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.33        12.33        25.25        12.00         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP 
       12.69        20.38         3.42         4.80        15.35        19.96 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7B 
       18.31         8.12        28.11        30.71        46.19        11.24 
TCGA-X8-AAAR 
       10.16 

$`2P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ 
       24.00         4.70        19.99        21.01         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       58.59         4.90        29.00         7.43         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U 
       83.24        46.09        12.66        12.43        13.41        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.10        13.25         0.10        22.39        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.22         4.47        10.52        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-R6-A8W5 
        0.13        33.11         5.16         7.82         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW 
        2.89         1.45         7.00        20.02         5.29         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EZ 
        4.44        18.81        22.82        12.43         1.55        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       42.87        15.06         9.17        15.91         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              0.1               0.1 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            53.95            122.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            12.33             13.05 
[1] "0.1 - 54.0 (12.3)"  "0.1 - 122.1 (13.1)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         1        3        3        1        10        11
  2P GAIN WILD-TYPE       7        2        4        0        29        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           6          1          3          2        2
  2P GAIN WILD-TYPE        19         11          7          5        3
                   vv
clus                STAGE IVA
  2P GAIN MUTATED           1
  2P GAIN WILD-TYPE         3
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 3                 2
  STAGE IB                 3                 4
  STAGE II                 1                 0
  STAGE IIA               10                29
  STAGE IIB               11                18
  STAGE III                6                19
  STAGE IIIA               1                11
  STAGE IIIB               3                 7
  STAGE IIIC               2                 5
  STAGE IV                 2                 3
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  2P GAIN MUTATED      13 10 23  0
  2P GAIN WILD-TYPE    18 26 62  5
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              13                18
  T2                 10                26
  T3                 23                62
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  2P GAIN MUTATED   21 19  3  3
  2P GAIN WILD-TYPE 50 45  9  5
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              21                50
  N1              19                45
  N2               3                 9
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   32  3
  2P GAIN WILD-TYPE 94  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     32    3
  2P GAIN WILD-TYPE   94    6
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              32                94
  1               3                 6
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     7  49
  2P GAIN WILD-TYPE  17 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      7   49
  2P GAIN WILD-TYPE   17  100
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               7                17
  MALE                49               100
[1] 2 2
[1] FALSE
D3V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED      18                         2    32
  2P GAIN WILD-TYPE    23                         0    79
D3V9, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                  18                23
  BLACK OR AFRICAN AMERICAN               2                 0
  WHITE                                  32                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    1 33
  2P GAIN WILD-TYPE  2 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   33
  2P GAIN WILD-TYPE    2   48
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              33                48
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   24 17
  2Q GAIN WILD-TYPE 76 54
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               130 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               17                54 
$`2Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RF TCGA-IG-A5S3 TCGA-JY-A6FA TCGA-JY-A93E 
       13.94         8.94         6.21        23.41        44.75        25.22 
TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OW TCGA-L5-A88V 
        4.31         3.68        32.61         3.32         7.13         2.60 
TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A4A1 
        0.36        55.50        52.57         5.92         0.10        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.49        12.59         0.10        12.33        25.25        12.00 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP 
        6.35        53.95        12.69         3.42         4.80        19.96 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA4D TCGA-X8-AAAR 
       18.31         8.12        28.11        46.19        10.16 

$`2Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB 
       14.86         4.67        14.50        12.16       122.10        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        0.30         8.94        24.00         4.70        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        4.90        29.00         7.43         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.95         3.02         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
       21.37         8.71        13.41        27.12        83.24        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       10.36        10.45        12.66        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
       15.35         0.10        13.25         0.10        12.46        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.16         7.04         9.30        15.78         2.89         1.45 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.02        20.38         5.29        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EY 
        4.44        18.81        22.82        12.43         1.55        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        42.87        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         2.66        19.73 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              0.1               0.1 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             55.5             122.1 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            12.00             12.87 
[1] "0.1 - 55.5 (12.0)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         1        1        2        1         6         9
  2Q GAIN WILD-TYPE       7        4        5        0        33        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           4          1          3          1        1
  2Q GAIN WILD-TYPE        21         11          7          6        4
                   vv
clus                STAGE IVA
  2Q GAIN MUTATED           1
  2Q GAIN WILD-TYPE         3
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 1                 4
  STAGE IB                 2                 5
  STAGE II                 1                 0
  STAGE IIA                6                33
  STAGE IIB                9                20
  STAGE III                4                21
  STAGE IIIA               1                11
  STAGE IIIB               3                 7
  STAGE IIIC               1                 6
  STAGE IV                 1                 4
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  2Q GAIN MUTATED      10  8 15  0
  2Q GAIN WILD-TYPE    21 28 70  5
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              10                21
  T2                  8                28
  T3                 15                70
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  2Q GAIN MUTATED   13 16  3  1
  2Q GAIN WILD-TYPE 58 48  9  7
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              13                58
  N1              16                48
  N2               3                 9
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    26   2
  2Q GAIN WILD-TYPE 100   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     26    2
  2Q GAIN WILD-TYPE  100    7
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              26               100
  1               2                 7
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4  38
  2Q GAIN WILD-TYPE  20 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   38
  2Q GAIN WILD-TYPE   20  111
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               4                20
  MALE                38               111
[1] 2 2
[1] FALSE
D4V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED      12                         1    25
  2Q GAIN WILD-TYPE    29                         1    86
D4V9, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                  12                29
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  25                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    1 23
  2Q GAIN WILD-TYPE  2 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   23
  2Q GAIN WILD-TYPE    2   58
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              23                58
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   12 16
  3P GAIN WILD-TYPE 88 55
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               28               143 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               16                55 
$`3P GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A4P3 TCGA-JY-A93C TCGA-JY-A93E 
       31.27        16.24         7.69        18.64        23.18        25.22 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A891 TCGA-L5-A8NE 
        0.30         4.31        47.93         3.16         3.95        55.50 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A1 
       27.12        52.57        10.36        10.45         0.10        12.59 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-AASW TCGA-VR-A8EQ 
        5.16         5.06        53.95        12.69         9.27        22.82 
TCGA-VR-A8ER TCGA-VR-A8EX TCGA-VR-AA7B TCGA-ZR-A9CJ 
       12.43        28.11        11.24        19.73 

$`3P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94         4.21        32.45         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       21.01        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         0.36         7.40         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       46.09         5.92        12.66        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35         0.10        13.25         0.10        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       12.00        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        6.35         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       20.02        20.38         5.29         3.42         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        4.44        18.81        19.96         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       30.71        18.18        42.87        46.19        15.06         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.91        10.16         3.42         2.10         2.66 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              0.1               0.1 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             55.5             122.1 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            12.64             12.49 
[1] "0.1 - 55.5 (12.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0        2        0        0         3         6
  3P GAIN WILD-TYPE       8        3        7        1        36        23
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           4          1          2          2        1
  3P GAIN WILD-TYPE        21         11          8          5        4
                   vv
clus                STAGE IVA
  3P GAIN MUTATED           2
  3P GAIN WILD-TYPE         2
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 2                 3
  STAGE IB                 0                 7
  STAGE II                 0                 1
  STAGE IIA                3                36
  STAGE IIB                6                23
  STAGE III                4                21
  STAGE IIIA               1                11
  STAGE IIIB               2                 8
  STAGE IIIC               2                 5
  STAGE IV                 1                 4
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3P GAIN MUTATED       5  3 15  1
  3P GAIN WILD-TYPE    26 33 70  4
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1               5                26
  T2                  3                33
  T3                 15                70
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3P GAIN MUTATED    7 12  2  3
  3P GAIN WILD-TYPE 64 52 10  5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               7                64
  N1              12                52
  N2               2                10
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    16   3
  3P GAIN WILD-TYPE 110   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     16    3
  3P GAIN WILD-TYPE  110    6
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              16               110
  1               3                 6
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3  25
  3P GAIN WILD-TYPE  21 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   25
  3P GAIN WILD-TYPE   21  124
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3                21
  MALE                25               124
[1] 2 2
[1] FALSE
D5V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       4                         0    20
  3P GAIN WILD-TYPE    37                         2    91
D5V9, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   4                37
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  20                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1 11
  3P GAIN WILD-TYPE  2 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   11
  3P GAIN WILD-TYPE    2   70
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              11                70
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   40 30
  3Q GAIN WILD-TYPE 60 41
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               70               101 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               30                41 
$`3Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 
       31.27        58.55         7.63        16.24         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         0.85         2.63        18.64         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43H 
       17.03        14.50        60.39        23.18        25.22         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
        4.31        47.93         3.16         7.13         6.94         2.60 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL 
        3.95        55.50         2.66        35.97        16.47        13.22 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L 
        8.71        13.41        27.12        52.57        10.36        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A1 
       12.43        13.41         0.10        13.15         0.10        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.33        10.52         5.16         8.02         7.59         5.06 
TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EQ 
       53.95        12.69        20.38         3.42         9.27        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
       12.43        18.31         8.12        28.11        30.71        42.87 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-ZR-A9CJ 
       15.06        11.24         9.17        19.73 

$`3Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A5B8 
       32.45         6.21        20.78        20.12         9.30         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       25.41        21.70        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
       58.59         4.90        29.00         7.43         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        0.36         7.40         3.02        12.92        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K 
        7.76         5.49        21.37        83.24        46.09         5.92 
TCGA-LN-A49M TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A6 
       12.66        15.35        13.25         0.10        12.46         0.10 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
       12.03        13.18         0.13        33.11         7.82        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        29.59         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        1.45         7.00        20.02         5.29         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EZ TCGA-VR-AA4D 
        4.44        18.81        19.96         1.55        18.18        46.19 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.91        10.16         3.42         2.10         2.66 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              0.1               0.1 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            60.39            122.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.59             12.46 
[1] "0.1 - 60.4 (12.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         2        2        2        0        14        11
  3Q GAIN WILD-TYPE       6        3        5        1        25        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED          13          6          4          3        2
  3Q GAIN WILD-TYPE        12          6          6          4        3
                   vv
clus                STAGE IVA
  3Q GAIN MUTATED           3
  3Q GAIN WILD-TYPE         1
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 2                 5
  STAGE II                 0                 1
  STAGE IIA               14                25
  STAGE IIB               11                18
  STAGE III               13                12
  STAGE IIIA               6                 6
  STAGE IIIB               4                 6
  STAGE IIIC               3                 4
  STAGE IV                 2                 3
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3Q GAIN MUTATED      10 11 40  2
  3Q GAIN WILD-TYPE    21 25 45  3
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              10                21
  T2                 11                25
  T3                 40                45
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3Q GAIN MUTATED   25 28  5  4
  3Q GAIN WILD-TYPE 46 36  7  4
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              25                46
  N1              28                36
  N2               5                 7
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   50  5
  3Q GAIN WILD-TYPE 76  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     50    5
  3Q GAIN WILD-TYPE   76    4
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              50                76
  1               5                 4
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    9 61
  3Q GAIN WILD-TYPE 15 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      9   61
  3Q GAIN WILD-TYPE   15   88
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               9                15
  MALE                61                88
[1] 2 2
[1] FALSE
D6V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED      19                         1    41
  3Q GAIN WILD-TYPE    22                         1    70
D6V9, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                  19                22
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  41                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    1 35
  3Q GAIN WILD-TYPE  2 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   35
  3Q GAIN WILD-TYPE    2   46
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              35                46
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   10  6
  4P GAIN WILD-TYPE 90 65
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               16               155 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6                65 
$`4P GAIN MUTATED`
TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-L5-A43J TCGA-L5-A4ON TCGA-L5-A8NE 
        2.63        23.41       122.10         4.31        18.35        55.50 
TCGA-L5-A8NV TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HY TCGA-R6-A6XG TCGA-R6-A6Y0 
       52.57        11.54         4.47        12.03        29.59        53.95 
TCGA-R6-A6Y2 TCGA-VR-A8EO TCGA-X8-AAAR TCGA-Z6-AAPN 
        9.30        18.81        10.16         2.66 

$`4P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        6.21        33.27        20.09         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
        6.28         3.16        30.25         0.30         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.68         4.70        32.61        19.99        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       83.24        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39         0.10        15.52        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-R6-A8W8 
        5.06        14.70         7.04         6.35        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        1.45        12.69         7.00        20.02        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        3.42         4.80        15.35         9.27         4.44        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        9.17        15.91         3.42         2.10        19.73 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             2.63              0.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           122.10             83.24 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            15.19             12.59 
[1] "2.6 - 122.1 (15.2)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.8"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         1        0        0        0         3         4
  4P GAIN WILD-TYPE       7        5        7        1        36        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           1          1          1          0        1
  4P GAIN WILD-TYPE        24         11          9          7        4
                   vv
clus                STAGE IVA
  4P GAIN MUTATED           0
  4P GAIN WILD-TYPE         4
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 0                 7
  STAGE II                 0                 1
  STAGE IIA                3                36
  STAGE IIB                4                25
  STAGE III                1                24
  STAGE IIIA               1                11
  STAGE IIIB               1                 9
  STAGE IIIC               0                 7
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  4P GAIN MUTATED       3  2  8  0
  4P GAIN WILD-TYPE    28 34 77  5
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               3                28
  T2                  2                34
  T3                  8                77
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4P GAIN MUTATED    7  6  0  0
  4P GAIN WILD-TYPE 64 58 12  8
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               7                64
  N1               6                58
  N2               0                12
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     9   1
  4P GAIN WILD-TYPE 117   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      9    1
  4P GAIN WILD-TYPE  117    8
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               9               117
  1               1                 8
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  15
  4P GAIN WILD-TYPE  23 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   15
  4P GAIN WILD-TYPE   23  134
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                23
  MALE                15               134
[1] 2 2
[1] FALSE
D7V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       3                         0    13
  4P GAIN WILD-TYPE    38                         2    98
D7V9, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   3                38
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  13                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  9
  4P GAIN WILD-TYPE  2 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    9
  4P GAIN WILD-TYPE    2   72
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               9                72
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   10  6
  4Q GAIN WILD-TYPE 90 65
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               155 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6                65 
$`4Q GAIN MUTATED`
TCGA-IG-A3YA TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A8NE 
       20.78        23.41       122.10         0.30        18.35        55.50 
TCGA-L5-A8NV TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HY TCGA-R6-A6Y0 TCGA-V5-A7RC 
       52.57        15.52        11.54        12.03        53.95         3.42 
TCGA-VR-A8EO TCGA-VR-A8EW TCGA-X8-AAAR TCGA-Z6-AAPN 
       18.81         8.12        10.16         2.66 

$`4Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
        6.21        33.27        20.09         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        6.28         3.16        30.25         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.68         4.70        32.61        19.99        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       83.24        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        22.39         0.10        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        5.06        14.70         7.04        29.59         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         4.80        15.35         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       19.96        22.82        12.43         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        9.17        15.91         3.42         2.10        19.73 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
              0.3               0.1 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           122.10             83.24 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           16.935            12.490 
[1] "0.3 - 122.1 (16.9)" "0.1 - 83.2 (12.5)" 
[1] "hr=" "1.8"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         1        0        0        0         4         3
  4Q GAIN WILD-TYPE       7        5        7        1        35        26
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           2          1          2          0        0
  4Q GAIN WILD-TYPE        23         11          8          7        5
                   vv
clus                STAGE IVA
  4Q GAIN MUTATED           0
  4Q GAIN WILD-TYPE         4
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 0                 7
  STAGE II                 0                 1
  STAGE IIA                4                35
  STAGE IIB                3                26
  STAGE III                2                23
  STAGE IIIA               1                11
  STAGE IIIB               2                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  4Q GAIN MUTATED       3  3  7  1
  4Q GAIN WILD-TYPE    28 33 78  4
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               3                28
  T2                  3                33
  T3                  7                78
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4Q GAIN MUTATED    8  5  1  0
  4Q GAIN WILD-TYPE 63 59 11  8
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               8                63
  N1               5                59
  N2               1                11
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    12   0
  4Q GAIN WILD-TYPE 114   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     12    0
  4Q GAIN WILD-TYPE  114    9
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              12               114
  1               0                 9
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  15
  4Q GAIN WILD-TYPE  23 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   15
  4Q GAIN WILD-TYPE   23  134
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                23
  MALE                15               134
[1] 2 2
[1] FALSE
D8V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       4                         1    11
  4Q GAIN WILD-TYPE    37                         1   100
D8V9, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   4                37
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  11               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  9
  4Q GAIN WILD-TYPE  3 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    9
  4Q GAIN WILD-TYPE    3   72
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               9                72
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   43 24
  5P GAIN WILD-TYPE 57 47
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               67               104 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               24                47 
$`5P GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC 
       14.30         5.92        32.45        33.27         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD 
       18.64         0.79        23.41        14.50        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J 
        3.68        42.77        31.56        25.22         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        8.94        32.61        19.99        47.93         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        3.16         4.90        29.00         7.13         6.94         0.36 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NV TCGA-L7-A6VZ 
       55.50        35.97        12.92        13.55        52.57        10.36 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
       13.41         0.10        13.25        12.46        12.59        12.59 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW 
        0.10        12.33        13.22         4.47        12.33        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 
       12.23        13.18         5.16         5.06        14.70        53.95 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EY 
        7.00        20.38         3.42        19.96        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       42.87        15.06        11.24        15.91         3.42         2.10 
TCGA-ZR-A9CJ 
       19.73 

$`5P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21         7.69         6.21        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
       20.78         3.88         9.30         0.53        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB 
        9.96        14.86         4.67        12.16       122.10        60.39 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        25.41        21.70        23.18        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ 
        3.16        30.25        24.00         3.68         4.70        21.01 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
       18.35         1.38        58.59         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI 
       25.12         7.40         3.95         3.02         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L 
       13.41        27.12        83.24        46.09         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.66        12.43        13.15        15.35         0.10         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 
       12.49        12.76        22.39        15.52        11.54        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       10.52        12.03         0.13        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.59         7.04        29.59         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         1.45        12.69        20.02         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         4.44        18.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7D 
        1.55        18.31         8.12        18.18        46.19         9.17 
TCGA-X8-AAAR TCGA-Z6-AAPN 
       10.16         2.66 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              0.1               0.1 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            68.02            122.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           13.180            12.295 
[1] "0.1 - 68.0 (13.2)"  "0.1 - 122.1 (12.3)"
[1] "hr=" "1.4"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         1        3        3        1        15        11
  5P GAIN WILD-TYPE       7        2        4        0        24        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED          10          6          2          5        4
  5P GAIN WILD-TYPE        15          6          8          2        1
                   vv
clus                STAGE IVA
  5P GAIN MUTATED           1
  5P GAIN WILD-TYPE         3
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 3                 2
  STAGE IB                 3                 4
  STAGE II                 1                 0
  STAGE IIA               15                24
  STAGE IIB               11                18
  STAGE III               10                15
  STAGE IIIA               6                 6
  STAGE IIIB               2                 8
  STAGE IIIC               5                 2
  STAGE IV                 4                 1
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  5P GAIN MUTATED       8 15 40  1
  5P GAIN WILD-TYPE    23 21 45  4
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1               8                23
  T2                 15                21
  T3                 40                45
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5P GAIN MUTATED   28 25  4  6
  5P GAIN WILD-TYPE 43 39  8  2
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              28                43
  N1              25                39
  N2               4                 8
  N3               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   48  5
  5P GAIN WILD-TYPE 78  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     48    5
  5P GAIN WILD-TYPE   78    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              48                78
  1               5                 4
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   13 55
  5P GAIN WILD-TYPE 11 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     13   55
  5P GAIN WILD-TYPE   11   94
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              13                11
  MALE                55                94
[1] 2 2
[1] FALSE
D9V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED      18                         1    43
  5P GAIN WILD-TYPE    23                         1    68
D9V9, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                  18                23
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  43                68
[1] 3 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, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    0 32
  5P GAIN WILD-TYPE  3 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0   32
  5P GAIN WILD-TYPE    3   49
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              32                49
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   15  4
  5Q GAIN WILD-TYPE 85 67
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               152 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                67 
$`5Q GAIN MUTATED`
TCGA-IG-A3I8 TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO 
       33.27        25.22         8.94        32.61        19.99         3.32 
TCGA-L5-A88S TCGA-L7-A6VZ TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4MR TCGA-LN-A7HW 
        6.94        10.36        12.46        12.59        13.22        12.00 
TCGA-LN-A7HX TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-AA7B 
       12.23         5.06        14.70         7.00         3.42        11.24 
TCGA-VR-AA7I 
       15.91 

$`5Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        6.21        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       24.00         3.68         4.70        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         7.43         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        5.49        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       10.52        12.03        13.18         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02         7.59         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.02        20.38         5.29         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        4.44        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       46.19        15.06         9.17        10.16         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             3.32              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            33.27            122.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           12.230            12.675 
[1] "3.3 - 33.3 (12.2)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.7"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         1        0        1        0         6         1
  5Q GAIN WILD-TYPE       7        5        6        1        33        28
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           1          1          0          3        1
  5Q GAIN WILD-TYPE        24         11         10          4        4
                   vv
clus                STAGE IVA
  5Q GAIN MUTATED           0
  5Q GAIN WILD-TYPE         4
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA                6                33
  STAGE IIB                1                28
  STAGE III                1                24
  STAGE IIIA               1                11
  STAGE IIIB               0                10
  STAGE IIIC               3                 4
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  5Q GAIN MUTATED       2  3 10  1
  5Q GAIN WILD-TYPE    29 33 75  4
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               2                29
  T2                  3                33
  T3                 10                75
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5Q GAIN MUTATED    9  2  1  4
  5Q GAIN WILD-TYPE 62 62 11  4
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               9                62
  N1               2                62
  N2               1                11
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    11   1
  5Q GAIN WILD-TYPE 115   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    1
  5Q GAIN WILD-TYPE  115    8
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              11               115
  1               1                 8
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     4  15
  5Q GAIN WILD-TYPE  20 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4   15
  5Q GAIN WILD-TYPE   20  134
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               4                20
  MALE                15               134
[1] 2 2
[1] FALSE
D10V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       5                         1    12
  5Q GAIN WILD-TYPE    36                         1    99
D10V9, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   5                36
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  12                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    0 11
  5Q GAIN WILD-TYPE  3 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   11
  5Q GAIN WILD-TYPE    3   70
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              11                70
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   20 16
  6P GAIN WILD-TYPE 80 55
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               36               135 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               16                55 
$`6P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63        13.94        16.24 
TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43E 
        3.88         4.67        14.50       122.10        68.02        30.25 
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
       47.93        58.59         6.94         2.60         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT 
       55.50         2.66        12.92         5.49        21.37        27.12 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ TCGA-LN-A7HW 
       10.36        10.45        13.15         0.10        12.33        12.00 
TCGA-LN-A7HX TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-VR-AA7I TCGA-Z6-A8JE 
       12.23        14.70         7.04        15.78        15.91         2.10 

$`6P GAIN WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       58.55         5.92         8.94         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA 
       23.41        12.82         9.96        14.86        12.16        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NI 
        8.71        25.12         0.36         7.40        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22         7.76         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        46.09         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
       13.41         0.10        15.35         0.10        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       10.52        12.03        13.18         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02         7.59         5.06        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       20.02        20.38         5.29         3.42         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       42.87        46.19        15.06        11.24         9.17        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.66        19.73 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              0.1               0.1 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           122.10             83.24 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           13.035            12.490 
[1] "0.1 - 122.1 (13.0)" "0.1 - 83.2 (12.5)" 
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         3        1        1        0         8         5
  6P GAIN WILD-TYPE       5        4        6        1        31        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           7          1          2          1        1
  6P GAIN WILD-TYPE        18         11          8          6        4
                   vv
clus                STAGE IVA
  6P GAIN MUTATED           3
  6P GAIN WILD-TYPE         1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 1                 4
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA                8                31
  STAGE IIB                5                24
  STAGE III                7                18
  STAGE IIIA               1                11
  STAGE IIIB               2                 8
  STAGE IIIC               1                 6
  STAGE IV                 1                 4
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  6P GAIN MUTATED       8  6 19  1
  6P GAIN WILD-TYPE    23 30 66  4
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1               8                23
  T2                  6                30
  T3                 19                66
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6P GAIN MUTATED   16 14  2  1
  6P GAIN WILD-TYPE 55 50 10  7
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              16                55
  N1              14                50
  N2               2                10
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    26   4
  6P GAIN WILD-TYPE 100   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     26    4
  6P GAIN WILD-TYPE  100    5
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              26               100
  1               4                 5
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     4  32
  6P GAIN WILD-TYPE  20 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4   32
  6P GAIN WILD-TYPE   20  117
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               4                20
  MALE                32               117
[1] 2 2
[1] FALSE
D11V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       9                         0    21
  6P GAIN WILD-TYPE    32                         2    90
D11V9, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   9                32
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  21                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    0 14
  6P GAIN WILD-TYPE  3 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   14
  6P GAIN WILD-TYPE    3   67
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              14                67
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   17 14
  6Q GAIN WILD-TYPE 83 57
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               31               140 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               14                57 
$`6Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS 
       31.27        14.30         7.63        13.94        16.24         3.88 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A88S 
       14.50       122.10        60.39        68.02        30.25         6.94 
TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NQ 
        2.60         3.02        55.50         2.66        12.92        21.37 
TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ 
       27.12        10.36        10.45        13.15         0.10        12.33 
TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-VR-AA7I 
        4.47        12.23        14.70         7.04        15.78        15.91 
TCGA-Z6-A8JE 
        2.10 

$`6Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78        58.55         5.92         8.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       12.16        44.75         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16         0.30         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
       29.00         7.13         7.43         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         3.95        35.97        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09         5.92        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
        0.10        15.35         0.10        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       11.54        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59         5.06        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        4.44        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD 
       46.19        15.06        11.24         9.17        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              0.1               0.1 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           122.10             83.24 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           13.150            12.475 
[1] "0.1 - 122.1 (13.2)" "0.1 - 83.2 (12.5)" 
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         4        0        1        0         7         4
  6Q GAIN WILD-TYPE       4        5        6        1        32        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           5          1          1          1        2
  6Q GAIN WILD-TYPE        20         11          9          6        3
                   vv
clus                STAGE IVA
  6Q GAIN MUTATED           3
  6Q GAIN WILD-TYPE         1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  4                 4
  STAGE IA                 0                 5
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA                7                32
  STAGE IIB                4                25
  STAGE III                5                20
  STAGE IIIA               1                11
  STAGE IIIB               1                 9
  STAGE IIIC               1                 6
  STAGE IV                 2                 3
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  6Q GAIN MUTATED       8  4 16  1
  6Q GAIN WILD-TYPE    23 32 69  4
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               8                23
  T2                  4                32
  T3                 16                69
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6Q GAIN MUTATED   15 11  1  1
  6Q GAIN WILD-TYPE 56 53 11  7
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              15                56
  N1              11                53
  N2               1                11
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    21   5
  6Q GAIN WILD-TYPE 105   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     21    5
  6Q GAIN WILD-TYPE  105    4
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              21               105
  1               5                 4
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  29
  6Q GAIN WILD-TYPE  22 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   29
  6Q GAIN WILD-TYPE   22  120
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               2                22
  MALE                29               120
[1] 2 2
[1] FALSE
D12V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       8                         0    18
  6Q GAIN WILD-TYPE    33                         2    93
D12V9, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   8                33
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  18                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    0 13
  6Q GAIN WILD-TYPE  3 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   13
  6Q GAIN WILD-TYPE    3   68
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              13                68
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   65 38
  7P GAIN WILD-TYPE 35 33
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              103                68 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               38                33 
$`7P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78         5.92        13.94         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
        7.69        20.09         2.63        20.12        18.64         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A939 
       17.03         0.79        23.41        14.50        60.39        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       23.18        25.22         3.16        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO 
       24.00         3.68         4.70        32.61        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S 
        1.38         3.16        58.59         4.90         7.13         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         0.36         3.95         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR 
       12.92        16.47        13.55        13.22         5.49         8.71 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       27.12        52.57        46.09        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41         0.10        15.35         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       12.59        12.49        12.76        12.59         0.10        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-Q9-A6FW 
       13.22        12.33        25.25        12.00         0.13         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35        53.95         9.30         1.45        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         3.42        15.35         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN 
       46.19        11.24        15.91        10.16         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`7P GAIN WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GQ TCGA-IC-A6RF 
       31.27        14.30        58.55         7.63         4.21         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 
       33.27         0.85        20.78         3.88         9.30        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D 
       68.02         3.68        41.52        42.77        25.41        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.03         6.28         8.94        19.99        21.01        47.93 
TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
        7.17        29.00         7.43         8.71        25.12         7.40 
TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       55.50        13.48         7.76        21.37        13.41        83.24 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A8 
       10.45        12.66        13.15        12.46        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       11.54         4.47        10.52        12.23        12.03        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-A7RE 
       33.11         5.16        15.78         2.89        20.02         4.80 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       18.81        22.82        12.43        18.18        42.87        15.06 
TCGA-VR-AA7D TCGA-Z6-A8JD 
        9.17         3.42 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.10              0.85 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            60.39            122.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           12.330            13.295 
[1] "0.1 - 60.4 (12.3)"  "0.8 - 122.1 (13.3)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         5        1        5        1        18        18
  7P GAIN WILD-TYPE       3        4        2        0        21        11
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          16          6          5          3        4
  7P GAIN WILD-TYPE         9          6          5          4        1
                   vv
clus                STAGE IVA
  7P GAIN MUTATED           3
  7P GAIN WILD-TYPE         1
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  5                 3
  STAGE IA                 1                 4
  STAGE IB                 5                 2
  STAGE II                 1                 0
  STAGE IIA               18                21
  STAGE IIB               18                11
  STAGE III               16                 9
  STAGE IIIA               6                 6
  STAGE IIIB               5                 5
  STAGE IIIC               3                 4
  STAGE IV                 4                 1
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  7P GAIN MUTATED      21 15 52  1
  7P GAIN WILD-TYPE    10 21 33  4
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              21                10
  T2                 15                21
  T3                 52                33
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   36 42  6  4
  7P GAIN WILD-TYPE 35 22  6  4
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              36                35
  N1              42                22
  N2               6                 6
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   67  7
  7P GAIN WILD-TYPE 59  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     67    7
  7P GAIN WILD-TYPE   59    2
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              67                59
  1               7                 2
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   11 93
  7P GAIN WILD-TYPE 13 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     11   93
  7P GAIN WILD-TYPE   13   56
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              11                13
  MALE                93                56
[1] 2 2
[1] FALSE
D13V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED      24                         2    68
  7P GAIN WILD-TYPE    17                         0    43
D13V9, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                  24                17
  BLACK OR AFRICAN AMERICAN               2                 0
  WHITE                                  68                43
[1] 3 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, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    3 50
  7P GAIN WILD-TYPE  0 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3   50
  7P GAIN WILD-TYPE    0   31
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 0
  NOT HISPANIC OR LATINO              50                31
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   53 30
  7Q GAIN WILD-TYPE 47 41
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               83                88 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               30                41 
$`7Q GAIN MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YC 
        8.94        16.24        32.45         7.69        20.09        20.12 
TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A939 
       18.64        17.03        23.41        14.50        60.39        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        25.22         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM 
        4.31        24.00         3.68         4.70        32.61        47.93 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
        3.32         3.16         4.90         6.94         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NN 
        3.95         3.02         2.66        35.97        13.22         5.49 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O 
       27.12        52.57        46.09        10.36         5.92        13.41 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        15.35         0.10        13.25        12.49        12.76 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10        15.52        11.54        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 
       25.25        12.00         0.13         7.82         8.02        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.04        29.59         6.35         9.30         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        15.35         9.27 
TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       19.96        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       46.19        11.24        10.16         2.10        19.73 

$`7Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       13.94         4.21         6.21        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 
        2.63         3.88         9.30         0.53         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F 
       68.02         3.68        41.52        42.77        25.41        24.03 
TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP 
        6.28         8.94        19.99        21.01        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        1.38        58.59        29.00         7.13         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       25.12         7.40        55.50        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55         7.76        21.37         8.71        13.41        83.24 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A49Y 
       10.45        12.66        12.43        13.15         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       12.59        12.59        22.39         4.47        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        13.18        33.11         5.16         7.59         5.06 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASX 
       53.95        15.78         2.89        20.02         4.80         4.44 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-VR-AA4G 
       18.81        22.82        12.43         1.55        42.87        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN 
        9.17        15.91         3.42         2.66 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.1               0.1 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            60.39            122.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            12.49             12.59 
[1] "0.1 - 60.4 (12.5)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         5        2        4        1        16        12
  7Q GAIN WILD-TYPE       3        3        3        0        23        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          10          3          5          5        3
  7Q GAIN WILD-TYPE        15          9          5          2        2
                   vv
clus                STAGE IVA
  7Q GAIN MUTATED           3
  7Q GAIN WILD-TYPE         1
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  5                 3
  STAGE IA                 2                 3
  STAGE IB                 4                 3
  STAGE II                 1                 0
  STAGE IIA               16                23
  STAGE IIB               12                17
  STAGE III               10                15
  STAGE IIIA               3                 9
  STAGE IIIB               5                 5
  STAGE IIIC               5                 2
  STAGE IV                 3                 2
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  7Q GAIN MUTATED      19 12 42  0
  7Q GAIN WILD-TYPE    12 24 43  5
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              19                12
  T2                 12                24
  T3                 42                43
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7Q GAIN MUTATED   32 29  5  6
  7Q GAIN WILD-TYPE 39 35  7  2
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              32                39
  N1              29                35
  N2               5                 7
  N3               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   53  6
  7Q GAIN WILD-TYPE 73  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     53    6
  7Q GAIN WILD-TYPE   73    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              53                73
  1               6                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7 77
  7Q GAIN WILD-TYPE 17 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7   77
  7Q GAIN WILD-TYPE   17   72
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               7                17
  MALE                77                72
[1] 2 2
[1] FALSE
D14V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED      21                         2    56
  7Q GAIN WILD-TYPE    20                         0    55
D14V9, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                  21                20
  BLACK OR AFRICAN AMERICAN               2                 0
  WHITE                                  56                55
[1] 3 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, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3 40
  7Q GAIN WILD-TYPE  0 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3   40
  7Q GAIN WILD-TYPE    0   41
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 0
  NOT HISPANIC OR LATINO              40                41
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   33 32
  8P GAIN WILD-TYPE 67 39
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               65               106 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32                39 
$`8P GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       14.30         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 
       20.09        20.78        17.03        12.82         4.67       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       68.02         3.68        31.56        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.30         4.31        19.99        47.93        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NG 
        3.16         4.90         7.13         2.60         0.36        35.97 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L7-A6VZ 
       13.55        13.22         7.76        21.37        13.41        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        5.92        10.45        13.41        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.25         0.10        12.59         0.10        12.03        13.18 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO 
        7.59         5.06         7.04        15.78        12.69         7.00 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EZ 
        4.80        15.35        19.96        22.82         8.12        18.18 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       46.19        11.24         3.42         2.10        19.73 

$`8P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
        7.69         6.21         0.85         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        3.88         9.30         0.53         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG 
       14.86        14.50        12.16        44.75        60.39        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-KH-A6WC 
       42.77        25.41        21.70        23.18        25.22         6.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        8.94        24.00         3.68         4.70        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.32         7.17        58.59        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        8.71        25.12         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR 
        2.66        12.92        13.48        16.47         5.49         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N 
       27.12        83.24        52.57        46.09        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
        0.10        12.46        12.59        12.49        12.76        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 
       25.25        10.52        12.00        12.23         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         7.82         8.02        14.70        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BV TCGA-S8-A6BW 
       53.95         9.30         2.89         1.45        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER 
        5.29         3.42         9.27         4.44        18.81        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G 
        1.55        18.31        28.11        30.71        42.87        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-AAPN 
        9.17        15.91        10.16         2.66 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              0.1               0.1 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           122.10             83.24 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           12.820            12.445 
[1] "0.1 - 122.1 (12.8)" "0.1 - 83.2 (12.4)" 
[1] "hr=" "1.5"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         2        2        3        1        13        10
  8P GAIN WILD-TYPE       6        3        4        0        26        19
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED          12          3          4          5        2
  8P GAIN WILD-TYPE        13          9          6          2        3
                   vv
clus                STAGE IVA
  8P GAIN MUTATED           2
  8P GAIN WILD-TYPE         2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 3                 4
  STAGE II                 1                 0
  STAGE IIA               13                26
  STAGE IIB               10                19
  STAGE III               12                13
  STAGE IIIA               3                 9
  STAGE IIIB               4                 6
  STAGE IIIC               5                 2
  STAGE IV                 2                 3
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8P GAIN MUTATED      10  9 40  1
  8P GAIN WILD-TYPE    21 27 45  4
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              10                21
  T2                  9                27
  T3                 40                45
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8P GAIN MUTATED   27 22  5  6
  8P GAIN WILD-TYPE 44 42  7  2
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              27                44
  N1              22                42
  N2               5                 7
  N3               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   45  4
  8P GAIN WILD-TYPE 81  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     45    4
  8P GAIN WILD-TYPE   81    5
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              45                81
  1               4                 5
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   10 55
  8P GAIN WILD-TYPE 14 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     10   55
  8P GAIN WILD-TYPE   14   94
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              10                14
  MALE                55                94
[1] 2 2
[1] FALSE
D15V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED      16                         1    42
  8P GAIN WILD-TYPE    25                         1    69
D15V9, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                  16                25
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  42                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    1 28
  8P GAIN WILD-TYPE  2 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   28
  8P GAIN WILD-TYPE    2   53
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              28                53
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   52 40
  8Q GAIN WILD-TYPE 48 31
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               92                79 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               40                31 
$`8Q GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
       14.30        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27        20.09        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        3.88        17.03        12.82         4.67        14.50       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C 
       68.02         3.68        23.18        31.56        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30         4.31        19.99        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         1.38         3.16         4.90         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.60         0.36        35.97        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        27.12        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.36         5.92        10.45        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 
       15.35         0.10        13.25         0.10        12.59        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        0.10        11.54        12.33        12.23        12.03        13.18 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG 
        7.59         5.06         7.04        53.95        15.78        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.02        20.38         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EY 
        4.44        19.96        22.82        12.43         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       18.18        46.19        11.24         9.17        15.91         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

$`8Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-IC-A6RF 
       25.78        31.27        58.55         7.63         5.92         6.21 
TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.85        18.64         9.30         0.53         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG 
        9.96        14.86        12.16        44.75        60.39        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43M 
       42.77        25.41        21.70        25.22         6.28         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP 
       24.00         3.68         4.70        32.61        21.01         7.17 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       58.59        29.00         6.94         8.71        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49Y 
       16.47        83.24        52.57        12.66        12.43        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.49        12.76        22.39        15.52        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A9FO TCGA-M9-A5M8 
       12.33        25.25        10.52        12.00         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         7.82         8.02        14.70        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC TCGA-VR-A8EO 
        9.30         2.89         1.45         5.29         3.42        18.81 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-X8-AAAR 
        1.55        18.31        28.11        42.87        15.06        10.16 
TCGA-Z6-AAPN 
        2.66 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.13 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           122.10             83.24 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.59             12.49 
[1] "0.1 - 122.1 (12.6)" "0.1 - 83.2 (12.5)" 
[1] "hr=" "1.3"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2        2        5        1        19        15
  8Q GAIN WILD-TYPE       6        3        2        0        20        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          18          6          6          7        2
  8Q GAIN WILD-TYPE         7          6          4          0        3
                   vv
clus                STAGE IVA
  8Q GAIN MUTATED           2
  8Q GAIN WILD-TYPE         2
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 5                 2
  STAGE II                 1                 0
  STAGE IIA               19                20
  STAGE IIB               15                14
  STAGE III               18                 7
  STAGE IIIA               6                 6
  STAGE IIIB               6                 4
  STAGE IIIC               7                 0
  STAGE IV                 2                 3
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8Q GAIN MUTATED      12 15 56  3
  8Q GAIN WILD-TYPE    19 21 29  2
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              12                19
  T2                 15                21
  T3                 56                29
  T4                  3                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   35 35  7  8
  8Q GAIN WILD-TYPE 36 29  5  0
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              35                36
  N1              35                29
  N2               7                 5
  N3               8                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   69  4
  8Q GAIN WILD-TYPE 57  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     69    4
  8Q GAIN WILD-TYPE   57    5
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              69                57
  1               4                 5
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   12 82
  8Q GAIN WILD-TYPE 12 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     12   82
  8Q GAIN WILD-TYPE   12   67
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              12                12
  MALE                82                67
[1] 2 2
[1] FALSE
D16V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED      25                         1    58
  8Q GAIN WILD-TYPE    16                         1    53
D16V9, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                  25                16
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  58                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    1 45
  8Q GAIN WILD-TYPE  2 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   45
  8Q GAIN WILD-TYPE    2   36
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              45                36
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    9  3
  9P GAIN WILD-TYPE 91 68
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               12               159 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                68 
$`9P GAIN MUTATED`
TCGA-2H-A9GL TCGA-IG-A625 TCGA-JY-A6F8 TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A8NT 
        5.92        12.82       122.10        29.00         0.36        27.12 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-VR-AA4G TCGA-VR-AA7D TCGA-Z6-AAPN 
       13.41         0.10         0.10        15.06         9.17         2.66 

$`9P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
        6.28         3.16        30.25         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       58.59         4.90         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.66        12.43        13.15        15.35        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       18.18        42.87        46.19        11.24        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        3.42         2.10        19.73 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              0.1               0.1 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           122.10             83.24 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           10.995            12.590 
[1] "0.1 - 122.1 (11.0)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.8"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         1        0        0        0         5         1
  9P GAIN WILD-TYPE       7        5        7        1        34        28
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           2          1          1          1        0
  9P GAIN WILD-TYPE        23         11          9          6        5
                   vv
clus                STAGE IVA
  9P GAIN MUTATED           0
  9P GAIN WILD-TYPE         4
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 0                 7
  STAGE II                 0                 1
  STAGE IIA                5                34
  STAGE IIB                1                28
  STAGE III                2                23
  STAGE IIIA               1                11
  STAGE IIIB               1                 9
  STAGE IIIC               1                 6
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  9P GAIN MUTATED       2  1 10  0
  9P GAIN WILD-TYPE    29 35 75  5
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               2                29
  T2                  1                35
  T3                 10                75
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9P GAIN MUTATED    8  2  2  1
  9P GAIN WILD-TYPE 63 62 10  7
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0               8                63
  N1               2                62
  N2               2                10
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    12   0
  9P GAIN WILD-TYPE 114   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     12    0
  9P GAIN WILD-TYPE  114    9
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              12               114
  1               0                 9
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  12
  9P GAIN WILD-TYPE  23 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   12
  9P GAIN WILD-TYPE   23  137
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               1                23
  MALE                12               137
[1] 2 2
[1] FALSE
D17V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       5                         0     6
  9P GAIN WILD-TYPE    36                         2   105
D17V9, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   5                36
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   6               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"
D17V10, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    0  6
  9P GAIN WILD-TYPE  3 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    6
  9P GAIN WILD-TYPE    3   75
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               6                75
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   19  8
  9Q GAIN WILD-TYPE 81 63
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               27               144 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8                63 
$`9Q GAIN MUTATED`
TCGA-2H-A9GL TCGA-IC-A6RE TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FB 
        5.92         7.69         0.53        12.82       122.10        60.39 
TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A8NT TCGA-LN-A49K 
        3.16         3.32        29.00         0.36        27.12         5.92 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A9 
       13.41         0.10         0.10         0.10        12.49        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-R6-A6L4 TCGA-S8-A6BV TCGA-VR-A8ER TCGA-VR-AA4D 
       12.33         4.47        14.70        20.02        12.43        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-Z6-AAPN 
       15.06         9.17         2.66 

$`9Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        3.88         9.30        17.03         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        83.24        52.57        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y 
       12.66        12.43        13.15        15.35        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
        9.27         4.44        18.81        19.96        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        30.71        18.18        42.87 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       11.24        15.91        10.16         3.42         2.10        19.73 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              0.1               0.1 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           122.10             83.24 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           11.540            12.725 
[1] "0.1 - 122.1 (11.5)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         2        0        1        0         9         3
  9Q GAIN WILD-TYPE       6        5        6        1        30        26
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           4          3          1          2        1
  9Q GAIN WILD-TYPE        21          9          9          5        4
                   vv
clus                STAGE IVA
  9Q GAIN MUTATED           0
  9Q GAIN WILD-TYPE         4
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 0                 5
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA                9                30
  STAGE IIB                3                26
  STAGE III                4                21
  STAGE IIIA               3                 9
  STAGE IIIB               1                 9
  STAGE IIIC               2                 5
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  9Q GAIN MUTATED       5  3 18  1
  9Q GAIN WILD-TYPE    26 33 67  4
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               5                26
  T2                  3                33
  T3                 18                67
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9Q GAIN MUTATED   13 10  2  2
  9Q GAIN WILD-TYPE 58 54 10  6
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              13                58
  N1              10                54
  N2               2                10
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    24   1
  9Q GAIN WILD-TYPE 102   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     24    1
  9Q GAIN WILD-TYPE  102    8
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              24               102
  1               1                 8
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  28
  9Q GAIN WILD-TYPE  23 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   28
  9Q GAIN WILD-TYPE   23  121
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               1                23
  MALE                28               121
[1] 2 2
[1] FALSE
D18V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED      13                         0    13
  9Q GAIN WILD-TYPE    28                         2    98
D18V9, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                  13                28
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  13                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    0 17
  9Q GAIN WILD-TYPE  3 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   17
  9Q GAIN WILD-TYPE    3   64
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              17                64
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   24 14
  10P GAIN WILD-TYPE 76 57
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                38                133 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                 57 
$`10P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       58.55        13.94        16.24        32.45         7.69         6.21 
TCGA-IG-A3YC TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OR 
       20.12       122.10        25.22         3.16        32.61         3.16 
TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NR 
        2.60         3.02        55.50        12.92        16.47         8.71 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A4A1 TCGA-LN-A4A6 
       10.36        10.45         0.10        13.15        12.59         0.10 
TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W5 
       12.33        12.23         8.02         5.06         6.35        15.78 
TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4D 
       20.38         9.27         1.55        18.31        42.87        46.19 
TCGA-X8-AAAR TCGA-Z6-A8JE 
       10.16         2.10 

$`10P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30         7.63         5.92         8.94 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        6.28        30.25         0.30         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68         4.70        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         7.43         6.94         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NK 
        7.40         3.95         2.66        35.97        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76         5.49        21.37        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        46.09         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.41        15.35         0.10        13.25         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04        29.59        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        2.89         1.45        12.69         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42         4.80        15.35         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       22.82        12.43         8.12        28.11        30.71        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.06        11.24         9.17        15.91         3.42         2.66 
TCGA-ZR-A9CJ 
       19.73 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               0.1                0.1 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            122.10              83.24 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             12.28              12.66 
[1] "0.1 - 122.1 (12.3)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.3"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         4        2        2        1         6         4
  10P GAIN WILD-TYPE       4        3        5        0        33        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           4          4          0          1        2
  10P GAIN WILD-TYPE        21          8         10          6        3
                    vv
clus                 STAGE IVA
  10P GAIN MUTATED           2
  10P GAIN WILD-TYPE         2
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  2                  3
  STAGE IB                  2                  5
  STAGE II                  1                  0
  STAGE IIA                 6                 33
  STAGE IIB                 4                 25
  STAGE III                 4                 21
  STAGE IIIA                4                  8
  STAGE IIIB                0                 10
  STAGE IIIC                1                  6
  STAGE IV                  2                  3
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  10P GAIN MUTATED      12  7 14  0
  10P GAIN WILD-TYPE    19 29 71  5
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1               12                 19
  T2                   7                 29
  T3                  14                 71
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10P GAIN MUTATED   15 17  0  1
  10P GAIN WILD-TYPE 56 47 12  7
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               15                 56
  N1               17                 47
  N2                0                 12
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    24   4
  10P GAIN WILD-TYPE 102   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     24    4
  10P GAIN WILD-TYPE  102    5
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               24                102
  1                4                  5
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3  35
  10P GAIN WILD-TYPE  21 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3   35
  10P GAIN WILD-TYPE   21  114
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                 21
  MALE                 35                114
[1] 2 2
[1] FALSE
D19V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       7                         0    26
  10P GAIN WILD-TYPE    34                         2    85
D19V9, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    7                 34
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   26                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    0 19
  10P GAIN WILD-TYPE  3 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   19
  10P GAIN WILD-TYPE    3   62
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               19                 62
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED   15 14
  10Q GAIN WILD-TYPE 85 57
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                29                142 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                 57 
$`10Q GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A5B8 
       58.55        13.94        16.24         7.69         6.21         0.79 
TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A893 
      122.10        25.22         4.31        32.61         3.16         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S 
       55.50        12.92        16.47        10.36        10.45        13.15 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W5 
        0.10        12.59         8.02         5.06         6.35        15.78 
TCGA-S8-A6BW TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-ZR-A9CJ 
       20.38        22.82        42.87        10.16        19.73 

$`10Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30         7.63         5.92         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.00         3.68         4.70        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG 
       25.12         0.36         7.40         3.95         2.66        35.97 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
        5.92        12.66        12.43        13.41         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25         0.10        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04        29.59        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        2.89         1.45        12.69         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.91         3.42         2.10         2.66 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               0.1                0.1 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            122.10              83.24 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            12.920             12.475 
[1] "0.1 - 122.1 (12.9)" "0.1 - 83.2 (12.5)" 
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         4        2        2        0         4         4
  10Q GAIN WILD-TYPE       4        3        5        1        35        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           2          2          0          2        1
  10Q GAIN WILD-TYPE        23         10         10          5        4
                    vv
clus                 STAGE IVA
  10Q GAIN MUTATED           2
  10Q GAIN WILD-TYPE         2
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  2                  3
  STAGE IB                  2                  5
  STAGE II                  0                  1
  STAGE IIA                 4                 35
  STAGE IIB                 4                 25
  STAGE III                 2                 23
  STAGE IIIA                2                 10
  STAGE IIIB                0                 10
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  10Q GAIN MUTATED      10  3 13  0
  10Q GAIN WILD-TYPE    21 33 72  5
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1               10                 21
  T2                   3                 33
  T3                  13                 72
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10Q GAIN MUTATED   14 10  0  2
  10Q GAIN WILD-TYPE 57 54 12  6
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               14                 57
  N1               10                 54
  N2                0                 12
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    17   3
  10Q GAIN WILD-TYPE 109   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     17    3
  10Q GAIN WILD-TYPE  109    6
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               17                109
  1                3                  6
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  27
  10Q GAIN WILD-TYPE  22 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   27
  10Q GAIN WILD-TYPE   22  122
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                 22
  MALE                 27                122
[1] 2 2
[1] FALSE
D20V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       4                         0    22
  10Q GAIN WILD-TYPE    37                         2    89
D20V9, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    4                 37
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   22                 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"
D20V10, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    0 15
  10Q GAIN WILD-TYPE  3 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   15
  10Q GAIN WILD-TYPE    3   66
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               15                 66
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED   15 21
  11P GAIN WILD-TYPE 85 50
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                36                135 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                21                 50 
$`11P GAIN MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB 
        8.94        16.24        23.41        14.50       122.10        60.39 
TCGA-JY-A6FE TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68         8.94        24.00         3.68        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV 
        1.38        29.00         2.66         5.49        27.12        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR 
       46.09         5.92         0.10        12.46        12.33        13.22 
TCGA-LN-A5U5 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-V5-A7RC 
        4.47         7.82         7.59         7.04         7.00         3.42 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA7I TCGA-ZR-A9CJ 
       22.82         8.12        30.71        18.18        15.91        19.73 

$`11P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       13.94         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        3.88         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86         4.67        12.16        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
        4.31         4.70        32.61        19.99        21.01         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       13.41        83.24        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       13.41         0.10        13.15        15.35        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       15.52        11.54        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.23        12.03        13.18         0.13        33.11         5.16 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         5.06        14.70        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
        9.30        15.78         2.89         1.45        12.69        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       18.81        19.96        12.43         1.55        18.31        28.11 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       42.87        46.19        15.06        11.24         9.17        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        3.42         2.10         2.66 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               0.1                0.1 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            122.10              83.24 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             12.84              12.59 
[1] "0.1 - 122.1 (12.8)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.3"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         2        1        1        0         9         6
  11P GAIN WILD-TYPE       6        4        6        1        30        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           6          1          3          2        1
  11P GAIN WILD-TYPE        19         11          7          5        4
                    vv
clus                 STAGE IVA
  11P GAIN MUTATED           2
  11P GAIN WILD-TYPE         2
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  4
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 9                 30
  STAGE IIB                 6                 23
  STAGE III                 6                 19
  STAGE IIIA                1                 11
  STAGE IIIB                3                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  11P GAIN MUTATED       7  4 23  1
  11P GAIN WILD-TYPE    24 32 62  4
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                7                 24
  T2                   4                 32
  T3                  23                 62
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11P GAIN MUTATED   15 12  5  2
  11P GAIN WILD-TYPE 56 52  7  6
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               15                 56
  N1               12                 52
  N2                5                  7
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    25   3
  11P GAIN WILD-TYPE 101   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     25    3
  11P GAIN WILD-TYPE  101    6
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               25                101
  1                3                  6
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6  32
  11P GAIN WILD-TYPE  18 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6   32
  11P GAIN WILD-TYPE   18  117
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                6                 18
  MALE                 32                117
[1] 2 2
[1] FALSE
D21V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED      10                         1    24
  11P GAIN WILD-TYPE    31                         1    87
D21V9, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                   10                 31
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   24                 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"
D21V10, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    0 16
  11P GAIN WILD-TYPE  3 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   16
  11P GAIN WILD-TYPE    3   65
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               16                 65
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED   16 12
  11Q GAIN WILD-TYPE 84 59
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                28                143 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                 59 
$`11Q GAIN MUTATED`
TCGA-IG-A51D TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43M 
       17.03        14.50       122.10        60.39         3.68         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU 
       24.00         3.68        32.61        18.35         1.38        29.00 
TCGA-L5-A88Y TCGA-L5-A8NN TCGA-LN-A49K TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.36         5.49         5.92        12.46        12.33        13.22 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-V5-AASW 
        7.82         7.59         7.04        15.78         7.00         9.27 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-ZR-A9CJ 
       22.82         8.12        30.71        19.73 

$`11Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       44.75        68.02        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
       30.25         0.30         4.31         4.70        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         3.32         7.17         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        11.54         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       12.00        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         8.02         5.06        14.70        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
       53.95         9.30         2.89         1.45        12.69        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
       20.38         5.29         3.42         4.80        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       18.81        19.96        12.43         1.55        18.31        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.91        10.16         3.42         2.10         2.66 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.36               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            122.10              83.24 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            12.395             12.590 
[1] "0.4 - 122.1 (12.4)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         3        0        0        0         6         5
  11Q GAIN WILD-TYPE       5        5        7        1        33        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           4          1          3          1        0
  11Q GAIN WILD-TYPE        21         11          7          6        5
                    vv
clus                 STAGE IVA
  11Q GAIN MUTATED           1
  11Q GAIN WILD-TYPE         3
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  0                  5
  STAGE IB                  0                  7
  STAGE II                  0                  1
  STAGE IIA                 6                 33
  STAGE IIB                 5                 24
  STAGE III                 4                 21
  STAGE IIIA                1                 11
  STAGE IIIB                3                  7
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  11Q GAIN MUTATED       8  3 15  0
  11Q GAIN WILD-TYPE    23 33 70  5
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                 23
  T2                   3                 33
  T3                  15                 70
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11Q GAIN MUTATED    9 10  5  1
  11Q GAIN WILD-TYPE 62 54  7  7
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                9                 62
  N1               10                 54
  N2                5                  7
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    18   1
  11Q GAIN WILD-TYPE 108   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     18    1
  11Q GAIN WILD-TYPE  108    8
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               18                108
  1                1                  8
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  25
  11Q GAIN WILD-TYPE  20 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   25
  11Q GAIN WILD-TYPE   20  124
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                4                 20
  MALE                 25                124
[1] 2 2
[1] FALSE
D22V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       7                         0    21
  11Q GAIN WILD-TYPE    34                         2    90
D22V9, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    7                 34
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   21                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    0 14
  11Q GAIN WILD-TYPE  3 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   14
  11Q GAIN WILD-TYPE    3   67
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               14                 67
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   31 21
  12P GAIN WILD-TYPE 69 50
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                52                119 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                21                 50 
$`12P GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L 
        7.63        16.24        20.09         2.63        18.64         0.53 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI 
       23.41         4.67         0.30         4.31        24.00        19.99 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NL 
       47.93         3.32         4.90         0.36         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        5.49        21.37        27.12        10.36         5.92        10.45 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 
        0.10        13.15         0.10        13.25        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.59         0.10        15.52        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG 
       25.25        13.18         0.13         8.02         7.59        29.59 
TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU 
       53.95        12.69        20.38        19.96         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-Z6-AAPN 
        8.12        28.11        42.87         2.66 

$`12P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        0.85        20.78        20.12         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        0.79        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         8.94         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        4.70        32.61        21.01        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         8.71        13.41        83.24        52.57        46.09 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       12.66        12.43        13.41        15.35         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HW 
       12.49        22.39        11.54        12.33        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6KZ 
       12.23        12.03        33.11         5.16         7.82         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       14.70         7.04         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        1.45         7.00        20.02         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         4.44        18.81        22.82        12.43 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10        19.73 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               0.1                0.1 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             53.95             122.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             12.59              12.49 
[1] "0.1 - 54.0 (12.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         0        1        1        1        14         6
  12P GAIN WILD-TYPE       8        4        6        0        25        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           8          3          4          3        3
  12P GAIN WILD-TYPE        17          9          6          4        2
                    vv
clus                 STAGE IVA
  12P GAIN MUTATED           3
  12P GAIN WILD-TYPE         1
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  1                  4
  STAGE IB                  1                  6
  STAGE II                  1                  0
  STAGE IIA                14                 25
  STAGE IIB                 6                 23
  STAGE III                 8                 17
  STAGE IIIA                3                  9
  STAGE IIIB                4                  6
  STAGE IIIC                3                  4
  STAGE IV                  3                  2
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  12P GAIN MUTATED       5 12 31  0
  12P GAIN WILD-TYPE    26 24 54  5
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1                5                 26
  T2                  12                 24
  T3                  31                 54
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  12P GAIN MUTATED   23 18  4  3
  12P GAIN WILD-TYPE 48 46  8  5
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               23                 48
  N1               18                 46
  N2                4                  8
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   35  6
  12P GAIN WILD-TYPE 91  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     35    6
  12P GAIN WILD-TYPE   91    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               35                 91
  1                6                  3
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3 50
  12P GAIN WILD-TYPE 21 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   50
  12P GAIN WILD-TYPE   21   99
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                3                 21
  MALE                 50                 99
[1] 2 2
[1] FALSE
D23V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED      21                         0    29
  12P GAIN WILD-TYPE    20                         2    82
D23V9, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                   21                 20
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   29                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1 30
  12P GAIN WILD-TYPE  2 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   30
  12P GAIN WILD-TYPE    2   51
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               30                 51
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   21 15
  12Q GAIN WILD-TYPE 79 56
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                135 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                 56 
$`12Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A4OE 
        7.63        16.24         2.63         0.53         4.67        24.00 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A8NL TCGA-L5-A8NN 
       47.93         3.32         4.90         0.36        13.22         5.49 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A49W 
       27.12        52.57        10.36        10.45         0.10        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.59         0.10        15.52        11.54        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A8WG 
       12.33        25.25         0.13         7.59        29.59        12.69 
TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       19.96        18.31        28.11        42.87         2.66        19.73 

$`12Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         4.31         8.94         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        19.99        21.01        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55         7.76        21.37         8.71        13.41        83.24 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       46.09         5.92        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35         0.10        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.59        22.39        13.22        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        13.18        33.11         5.16         7.82         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        14.70         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         2.89         1.45         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY 
       18.81        22.82        12.43         1.55         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       10.16         3.42         2.10 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               0.1                0.1 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             52.57             122.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             12.33              12.66 
[1] "0.1 - 52.6 (12.3)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0        1        0        1         9         2
  12Q GAIN WILD-TYPE       8        4        7        0        30        27
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           5          3          3          3        3
  12Q GAIN WILD-TYPE        20          9          7          4        2
                    vv
clus                 STAGE IVA
  12Q GAIN MUTATED           2
  12Q GAIN WILD-TYPE         2
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  1                  4
  STAGE IB                  0                  7
  STAGE II                  1                  0
  STAGE IIA                 9                 30
  STAGE IIB                 2                 27
  STAGE III                 5                 20
  STAGE IIIA                3                  9
  STAGE IIIB                3                  7
  STAGE IIIC                3                  4
  STAGE IV                  3                  2
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  12Q GAIN MUTATED       4  7 22  0
  12Q GAIN WILD-TYPE    27 29 63  5
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                4                 27
  T2                   7                 29
  T3                  22                 63
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  12Q GAIN MUTATED   13 14  3  3
  12Q GAIN WILD-TYPE 58 50  9  5
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               13                 58
  N1               14                 50
  N2                3                  9
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    23   5
  12Q GAIN WILD-TYPE 103   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     23    5
  12Q GAIN WILD-TYPE  103    4
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               23                103
  1                5                  4
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  34
  12Q GAIN WILD-TYPE  22 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   34
  12Q GAIN WILD-TYPE   22  115
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 22
  MALE                 34                115
[1] 2 2
[1] FALSE
D24V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED      14                         0    19
  12Q GAIN WILD-TYPE    27                         2    92
D24V9, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                   14                 27
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   19                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1 19
  12Q GAIN WILD-TYPE  2 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   19
  12Q GAIN WILD-TYPE    2   62
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               19                 62
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   22 18
  13Q GAIN WILD-TYPE 78 53
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                40                131 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                18                 53 
$`13Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A5B8 TCGA-IG-A97H 
       31.27        14.30         5.92        13.94         0.79        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C 
      122.10         3.68        42.77        23.18        31.56         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OQ 
       30.25         8.94         4.70        19.99         7.17         1.38 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        7.13         2.60         0.36         3.02         2.66        12.92 
TCGA-L5-A8NT TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-Q9-A6FW TCGA-R6-A6L4 
       27.12        12.33        25.25        12.00         7.82        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        7.04         9.30        15.78        20.02         5.29         3.42 
TCGA-V5-AASW TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ 
        9.27        46.19        10.16        19.73 

$`13Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        58.55         7.63         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       32.45         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
        4.67        12.16        44.75        60.39        68.02        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H 
       25.41        21.70        25.22        24.03         6.28         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31        24.00         3.68        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43         6.94         8.71        25.12         7.40         3.95 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50        35.97        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.59        22.39         0.10        15.52        11.54        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        33.11         5.16         8.02         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       29.59         6.35        53.95         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        7.00        20.38         4.80        15.35         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        30.71        18.18        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91         3.42         2.10         2.66 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.36               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            122.10              83.24 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             11.08              12.66 
[1] "0.4 - 122.1 (11.1)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         4        1        2        0         3         5
  13Q GAIN WILD-TYPE       4        4        5        1        36        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           5          2          2          3        1
  13Q GAIN WILD-TYPE        20         10          8          4        4
                    vv
clus                 STAGE IVA
  13Q GAIN MUTATED           2
  13Q GAIN WILD-TYPE         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  4
  STAGE IB                  2                  5
  STAGE II                  0                  1
  STAGE IIA                 3                 36
  STAGE IIB                 5                 24
  STAGE III                 5                 20
  STAGE IIIA                2                 10
  STAGE IIIB                2                  8
  STAGE IIIC                3                  4
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  13Q GAIN MUTATED      13  6 15  0
  13Q GAIN WILD-TYPE    18 30 70  5
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               13                 18
  T2                   6                 30
  T3                  15                 70
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  13Q GAIN MUTATED   12 14  4  3
  13Q GAIN WILD-TYPE 59 50  8  5
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               12                 59
  N1               14                 50
  N2                4                  8
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    21   3
  13Q GAIN WILD-TYPE 105   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     21    3
  13Q GAIN WILD-TYPE  105    6
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               21                105
  1                3                  6
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5  35
  13Q GAIN WILD-TYPE  19 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   35
  13Q GAIN WILD-TYPE   19  114
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                5                 19
  MALE                 35                114
[1] 2 2
[1] FALSE
D25V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       5                         1    27
  13Q GAIN WILD-TYPE    36                         1    84
D25V9, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    5                 36
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   27                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2 14
  13Q GAIN WILD-TYPE  1 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   14
  13Q GAIN WILD-TYPE    1   67
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               14                 67
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   27 16
  14Q GAIN WILD-TYPE 73 55
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                43                128 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                 55 
$`14Q GAIN MUTATED`
TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A6QS TCGA-IG-A97I 
        5.92         0.85        20.78        18.64         9.96        12.16 
TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OR TCGA-L5-A4OX 
       23.18         3.16        30.25         4.31         3.16         7.43 
TCGA-L5-A8NG TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49S 
       35.97         5.49        21.37        13.41         5.92        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A9 
       15.35         0.10         0.10        12.59        12.59        11.54 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       13.22        12.33        25.25        12.03        13.18         0.13 
TCGA-R6-A6DN TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASX TCGA-VR-A8EW 
        8.02        53.95        20.02        20.38         4.44         8.12 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       46.19        11.24         9.17        15.91         3.42         2.10 
TCGA-ZR-A9CJ 
       19.73 

$`14Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27        20.09         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
        0.53        17.03         0.79        23.41        12.82        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        4.67        14.50       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
        3.68        41.52        42.77        25.41        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
       25.22        24.03         6.28         0.30         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.68         4.70        32.61        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W 
       10.45        12.66        12.43        13.41         0.10        13.25 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.49        12.76        22.39         0.10        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-M9-A5M8 
       12.33         4.47        10.52        12.00        12.23        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       29.59         6.35         9.30        15.78         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00         5.29         3.42         4.80        15.35 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       18.31        28.11        30.71        18.18        42.87        15.06 
TCGA-X8-AAAR TCGA-Z6-AAPN 
       10.16         2.66 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               0.1                0.1 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             53.95             122.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            12.160             12.725 
[1] "0.1 - 54.0 (12.2)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         1        1        2        0        13         8
  14Q GAIN WILD-TYPE       7        4        5        1        26        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           6          4          2          2        1
  14Q GAIN WILD-TYPE        19          8          8          5        4
                    vv
clus                 STAGE IVA
  14Q GAIN MUTATED           0
  14Q GAIN WILD-TYPE         4
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  4
  STAGE IB                  2                  5
  STAGE II                  0                  1
  STAGE IIA                13                 26
  STAGE IIB                 8                 21
  STAGE III                 6                 19
  STAGE IIIA                4                  8
  STAGE IIIB                2                  8
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  14Q GAIN MUTATED       3 13 21  3
  14Q GAIN WILD-TYPE    28 23 64  2
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                3                 28
  T2                  13                 23
  T3                  21                 64
  T4                   3                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  14Q GAIN MUTATED   22 13  2  3
  14Q GAIN WILD-TYPE 49 51 10  5
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               22                 49
  N1               13                 51
  N2                2                 10
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   34  1
  14Q GAIN WILD-TYPE 92  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     34    1
  14Q GAIN WILD-TYPE   92    8
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               34                 92
  1                1                  8
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  43
  14Q GAIN WILD-TYPE  23 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   43
  14Q GAIN WILD-TYPE   23  106
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                1                 23
  MALE                 43                106
[1] 2 2
[1] FALSE
D26V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED      17                         0    25
  14Q GAIN WILD-TYPE    24                         2    86
D26V9, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                   17                 24
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   25                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    0 28
  14Q GAIN WILD-TYPE  3 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   28
  14Q GAIN WILD-TYPE    3   53
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               28                 53
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   15 12
  15Q GAIN WILD-TYPE 85 59
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                27                144 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                 59 
$`15Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A50L TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43C 
        7.63         8.94         0.53       122.10        60.39         3.16 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NJ 
        3.16         7.13         6.94         2.60         0.36        16.47 
TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4MR TCGA-LN-A7HW TCGA-LN-A7HX 
       46.09        10.45         0.10        13.22        12.00        12.23 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-VR-A8EP 
       33.11         7.82         7.59         7.04         6.35        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-AA7D 
       22.82         1.55         9.17 

$`15Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       16.24         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38        58.59         4.90        29.00         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        8.71        25.12         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        11.54        12.33         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU 
       25.25        10.52        12.03        13.18         0.13         5.16 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         5.06        14.70        29.59        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
        4.44        18.81        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10         2.66        19.73 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               0.1                0.1 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            122.10              83.24 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              7.82              12.87 
[1] "0.1 - 122.1 (7.8)" "0.1 - 83.2 (12.9)"
[1] "hr=" "1.2"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         2        1        2        0         6         1
  15Q GAIN WILD-TYPE       6        4        5        1        33        28
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           6          1          2          1        0
  15Q GAIN WILD-TYPE        19         11          8          6        5
                    vv
clus                 STAGE IVA
  15Q GAIN MUTATED           0
  15Q GAIN WILD-TYPE         4
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  4
  STAGE IB                  2                  5
  STAGE II                  0                  1
  STAGE IIA                 6                 33
  STAGE IIB                 1                 28
  STAGE III                 6                 19
  STAGE IIIA                1                 11
  STAGE IIIB                2                  8
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  15Q GAIN MUTATED       4  7 12  0
  15Q GAIN WILD-TYPE    27 29 73  5
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1                4                 27
  T2                   7                 29
  T3                  12                 73
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  15Q GAIN MUTATED   11  9  2  1
  15Q GAIN WILD-TYPE 60 55 10  7
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               11                 60
  N1                9                 55
  N2                2                 10
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    19   0
  15Q GAIN WILD-TYPE 107   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     19    0
  15Q GAIN WILD-TYPE  107    9
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               19                107
  1                0                  9
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2  25
  15Q GAIN WILD-TYPE  22 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   25
  15Q GAIN WILD-TYPE   22  124
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                2                 22
  MALE                 25                124
[1] 2 2
[1] FALSE
D27V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       6                         0    16
  15Q GAIN WILD-TYPE    35                         2    95
D27V9, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    6                 35
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   16                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    0 10
  15Q GAIN WILD-TYPE  3 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   10
  15Q GAIN WILD-TYPE    3   71
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               10                 71
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   22 15
  16P GAIN WILD-TYPE 78 56
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                37                134 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                 56 
$`16P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-IG-A97H 
       58.55         0.85         0.53         0.79         4.67        14.50 
TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF 
        0.30         3.32        29.00         6.94        55.50         2.66 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49S 
       21.37        13.41        27.12        10.36         5.92        13.15 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
       13.25        12.59        12.76        12.59         0.10        11.54 
TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W5 
       12.33        12.03         0.13         5.06        29.59        15.78 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-Z6-A8JD 
       20.38        15.35        12.43         8.12        28.11         3.42 
TCGA-ZR-A9CJ 
       19.73 

$`16P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        3.16        58.59         4.90         7.13         7.43         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         5.49         8.71        83.24        52.57        46.09 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.45        12.66        12.43        13.41         0.10        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.10        12.46        12.49        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.23        13.18        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        2.89         1.45        12.69         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42         4.80         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       22.82         1.55        18.31        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JE TCGA-Z6-AAPN 
        2.10         2.66 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               0.1                0.1 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             58.55             122.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            12.430             12.675 
[1] "0.1 - 58.5 (12.4)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.2"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         1        0        3        1         8         6
  16P GAIN WILD-TYPE       7        5        4        0        31        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           6          2          2          3        0
  16P GAIN WILD-TYPE        19         10          8          4        5
                    vv
clus                 STAGE IVA
  16P GAIN MUTATED           3
  16P GAIN WILD-TYPE         1
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  3                  4
  STAGE II                  1                  0
  STAGE IIA                 8                 31
  STAGE IIB                 6                 23
  STAGE III                 6                 19
  STAGE IIIA                2                 10
  STAGE IIIB                2                  8
  STAGE IIIC                3                  4
  STAGE IV                  0                  5
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  16P GAIN MUTATED       3  7 23  2
  16P GAIN WILD-TYPE    28 29 62  3
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                3                 28
  T2                   7                 29
  T3                  23                 62
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16P GAIN MUTATED   18 11  2  3
  16P GAIN WILD-TYPE 53 53 10  5
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               18                 53
  N1               11                 53
  N2                2                 10
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   27  3
  16P GAIN WILD-TYPE 99  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     27    3
  16P GAIN WILD-TYPE   99    6
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               27                 99
  1                3                  6
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  37
  16P GAIN WILD-TYPE  24 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   37
  16P GAIN WILD-TYPE   24  112
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                0                 24
  MALE                 37                112
[1] 2 2
[1] FALSE
D28V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED      15                         1    18
  16P GAIN WILD-TYPE    26                         1    93
D28V9, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                   15                 26
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   18                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    0 23
  16P GAIN WILD-TYPE  3 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   23
  16P GAIN WILD-TYPE    3   58
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               23                 58
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   19 16
  16Q GAIN WILD-TYPE 81 55
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                35                136 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                 55 
$`16Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A43J 
       13.94         0.85         0.79         4.67         0.30         4.31 
TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NF TCGA-L5-A8NQ TCGA-L5-A8NS 
        3.32        29.00         6.94         2.66        21.37        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49R TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 
       27.12        52.57         0.10        12.59        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6XG 
        0.10        11.54        12.33        12.03         0.13        29.59 
TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8EW 
       15.78        20.38         3.42        15.35        12.43         8.12 
TCGA-VR-A8EX TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       28.11        11.24         3.42         2.10        19.73 

$`16Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16        30.25         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       32.61        19.99        21.01        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU 
       13.55        13.22         7.76         5.49         8.71        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.46        12.49        22.39        15.52        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        25.25        10.52        12.00        12.23        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       33.11         5.16         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       14.70         7.04         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        1.45        12.69         7.00        20.02         5.29         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
        9.27         4.44        18.81        19.96        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-AAPN 
        9.17        15.91        10.16         2.66 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               0.1                0.1 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             52.57             122.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             12.03              12.87 
[1] "0.1 - 52.6 (12.0)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "1.7"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0        0        3        1         6         7
  16Q GAIN WILD-TYPE       8        5        4        0        33        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           6          2          2          2        1
  16Q GAIN WILD-TYPE        19         10          8          5        4
                    vv
clus                 STAGE IVA
  16Q GAIN MUTATED           3
  16Q GAIN WILD-TYPE         1
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  3                  4
  STAGE II                  1                  0
  STAGE IIA                 6                 33
  STAGE IIB                 7                 22
  STAGE III                 6                 19
  STAGE IIIA                2                 10
  STAGE IIIB                2                  8
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  16Q GAIN MUTATED       3  6 22  2
  16Q GAIN WILD-TYPE    28 30 63  3
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                3                 28
  T2                   6                 30
  T3                  22                 63
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16Q GAIN MUTATED   17 11  2  3
  16Q GAIN WILD-TYPE 54 53 10  5
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               17                 54
  N1               11                 53
  N2                2                 10
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    24   4
  16Q GAIN WILD-TYPE 102   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     24    4
  16Q GAIN WILD-TYPE  102    5
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               24                102
  1                4                  5
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  34
  16Q GAIN WILD-TYPE  23 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   34
  16Q GAIN WILD-TYPE   23  115
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                1                 23
  MALE                 34                115
[1] 2 2
[1] FALSE
D29V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED      11                         2    19
  16Q GAIN WILD-TYPE    30                         0    92
D29V9, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                   11                 30
  BLACK OR AFRICAN AMERICAN                2                  0
  WHITE                                   19                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    0 20
  16Q GAIN WILD-TYPE  3 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   20
  16Q GAIN WILD-TYPE    3   61
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               20                 61
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   18 11
  17P GAIN WILD-TYPE 82 60
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                29                142 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                 60 
$`17P GAIN MUTATED`
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-JY-A6FB TCGA-JY-A93C 
        7.69        20.09         0.53        17.03        60.39        23.18 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A88Z 
       25.22         0.30         4.31        18.35         1.38         7.40 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A2 
       55.50        35.97        13.41         0.10         0.10        12.49 
TCGA-LN-A4A4 TCGA-LN-A7HW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-V5-A7RC TCGA-VR-A8ET 
       12.59        12.00         8.02         5.06         3.42         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7I TCGA-Z6-A8JE 
       18.31        30.71        46.19        15.91         2.10 

$`17P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF 
       13.94         8.94        16.24         4.21        32.45         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
       31.56        24.03         6.28         3.16        30.25         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         3.32         7.17         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         0.36         3.95         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.02        20.38         5.29         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW 
        4.44        18.81        19.96        22.82        12.43         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        18.18        42.87        15.06        11.24         9.17 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       10.16         3.42         2.66        19.73 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               0.1                0.1 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             60.39             122.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            12.490             12.625 
[1] "0.1 - 60.4 (12.5)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         1        0        1        0         7         7
  17P GAIN WILD-TYPE       7        5        6        1        32        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           5          4          1          0        1
  17P GAIN WILD-TYPE        20          8          9          7        4
                    vv
clus                 STAGE IVA
  17P GAIN MUTATED           0
  17P GAIN WILD-TYPE         4
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 7                 32
  STAGE IIB                 7                 22
  STAGE III                 5                 20
  STAGE IIIA                4                  8
  STAGE IIIB                1                  9
  STAGE IIIC                0                  7
  STAGE IV                  1                  4
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  17P GAIN MUTATED       7  5 14  1
  17P GAIN WILD-TYPE    24 31 71  4
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1                7                 24
  T2                   5                 31
  T3                  14                 71
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17P GAIN MUTATED   10 15  2  0
  17P GAIN WILD-TYPE 61 49 10  8
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               10                 61
  N1               15                 49
  N2                2                 10
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    23   1
  17P GAIN WILD-TYPE 103   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     23    1
  17P GAIN WILD-TYPE  103    8
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               23                103
  1                1                  8
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     2  28
  17P GAIN WILD-TYPE  22 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2   28
  17P GAIN WILD-TYPE   22  121
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 22
  MALE                 28                121
[1] 2 2
[1] FALSE
D30V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       9                         1    20
  17P GAIN WILD-TYPE    32                         1    91
D30V9, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    9                 32
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   20                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0 15
  17P GAIN WILD-TYPE  3 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   15
  17P GAIN WILD-TYPE    3   66
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               15                 66
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   25 15
  17Q GAIN WILD-TYPE 75 56
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                40                131 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                 56 
$`17Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A93C 
       20.09         0.53        17.03        12.82        60.39        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4ON 
       31.56        25.22        30.25         0.30        24.00        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG 
        3.32         1.38         4.90         7.40        55.50        35.97 
TCGA-L5-A8NN TCGA-L5-A8NT TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A2 
        5.49        27.12         0.10        13.15         0.10        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A7HW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.76        12.59        12.00         8.02         7.59         5.06 
TCGA-R6-A6XG TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8ET TCGA-VR-A8EU 
       29.59         3.42        15.35         9.27         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7I TCGA-Z6-A8JE 
       30.71        46.19        15.91         2.10 

$`17Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        6.21        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       18.64         3.88         9.30         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF 
       24.03         6.28         3.16         4.31         8.94         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP 
        4.70        32.61        19.99        21.01        47.93         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         0.36         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.41        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 
       13.18         0.13        33.11         5.16         7.82        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        1.45        12.69         7.00        20.02        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        4.80         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        18.18        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        10.16         3.42         2.66        19.73 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               0.1                0.1 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             60.39             122.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             12.79              12.43 
[1] "0.1 - 60.4 (12.8)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         2        0        1        0         7         7
  17Q GAIN WILD-TYPE       6        5        6        1        32        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           7          4          3          2        2
  17Q GAIN WILD-TYPE        18          8          7          5        3
                    vv
clus                 STAGE IVA
  17Q GAIN MUTATED           0
  17Q GAIN WILD-TYPE         4
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  0                  5
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 7                 32
  STAGE IIB                 7                 22
  STAGE III                 7                 18
  STAGE IIIA                4                  8
  STAGE IIIB                3                  7
  STAGE IIIC                2                  5
  STAGE IV                  2                  3
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  17Q GAIN MUTATED       7  6 21  1
  17Q GAIN WILD-TYPE    24 30 64  4
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1                7                 24
  T2                   6                 30
  T3                  21                 64
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17Q GAIN MUTATED   12 17  4  2
  17Q GAIN WILD-TYPE 59 47  8  6
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               12                 59
  N1               17                 47
  N2                4                  8
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   29  2
  17Q GAIN WILD-TYPE 97  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     29    2
  17Q GAIN WILD-TYPE   97    7
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               29                 97
  1                2                  7
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     3  38
  17Q GAIN WILD-TYPE  21 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3   38
  17Q GAIN WILD-TYPE   21  111
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 21
  MALE                 38                111
[1] 2 2
[1] FALSE
D31V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED      11                         2    28
  17Q GAIN WILD-TYPE    30                         0    83
D31V9, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                   11                 30
  BLACK OR AFRICAN AMERICAN                2                  0
  WHITE                                   28                 83
[1] 3 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, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0 20
  17Q GAIN WILD-TYPE  3 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   20
  17Q GAIN WILD-TYPE    3   61
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               20                 61
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   25 23
  18P GAIN WILD-TYPE 75 48
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                48                123 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                23                 48 
$`18P GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A97I 
        7.63        13.94         4.21         0.53        12.82        12.16 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4ON 
       60.39         3.68        25.41         4.31        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NL 
        1.38         3.16         4.90         7.13         0.36        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37        13.41        27.12        83.24        46.09 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 
       13.15        15.35         0.10        13.25         0.10        12.76 
TCGA-LN-A4A4 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.59        12.33        13.22         4.47        12.33        25.25 
TCGA-R6-A6KZ TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EQ 
        5.06        12.69        20.38         3.42         4.80        22.82 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE 
       28.11        18.18        42.87        11.24        15.91         2.10 

$`18P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30        17.03         0.79        23.41         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        4.67        14.50       122.10        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
        6.28         3.16        30.25         0.30         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
        3.68         4.70        32.61        19.99        21.01         3.32 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        7.17        58.59        29.00         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        7.76         8.71        52.57        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 
       12.66        12.43        13.41         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV 
       12.49        22.39         0.10        15.52        11.54        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       12.00        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        1.45         7.00        20.02         5.29        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
        8.12        30.71        46.19        15.06         9.17        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.66        19.73 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               0.1                0.1 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             83.24             122.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            12.725             12.460 
[1] "0.1 - 83.2 (12.7)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.3"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         1        2        3        0         9         9
  18P GAIN WILD-TYPE       7        3        4        1        30        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED          11          4          1          1        3
  18P GAIN WILD-TYPE        14          8          9          6        2
                    vv
clus                 STAGE IVA
  18P GAIN MUTATED           1
  18P GAIN WILD-TYPE         3
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  2                  3
  STAGE IB                  3                  4
  STAGE II                  0                  1
  STAGE IIA                 9                 30
  STAGE IIB                 9                 20
  STAGE III                11                 14
  STAGE IIIA                4                  8
  STAGE IIIB                1                  9
  STAGE IIIC                1                  6
  STAGE IV                  3                  2
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18P GAIN MUTATED       8 11 26  1
  18P GAIN WILD-TYPE    23 25 59  4
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                8                 23
  T2                  11                 25
  T3                  26                 59
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18P GAIN MUTATED   20 22  2  2
  18P GAIN WILD-TYPE 51 42 10  6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               20                 51
  N1               22                 42
  N2                2                 10
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   35  4
  18P GAIN WILD-TYPE 91  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     35    4
  18P GAIN WILD-TYPE   91    5
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               35                 91
  1                4                  5
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3  46
  18P GAIN WILD-TYPE  21 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3   46
  18P GAIN WILD-TYPE   21  103
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 21
  MALE                 46                103
[1] 2 2
[1] FALSE
D32V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED      15                         1    28
  18P GAIN WILD-TYPE    26                         1    83
D32V9, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                   15                 26
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   28                 83
[1] 3 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, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1 20
  18P GAIN WILD-TYPE  2 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   20
  18P GAIN WILD-TYPE    2   61
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               20                 61
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   13 12
  18Q GAIN WILD-TYPE 87 59
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                25                146 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                 59 
$`18Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A625 
        7.63         5.92        13.94         4.21        33.27        12.82 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43E TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88Y 
       60.39         3.68        30.25         3.16         7.13         0.36 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HY 
       13.22         5.49        21.37         0.10        12.76        12.03 
TCGA-R6-A6KZ TCGA-S8-A6BW TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I 
        5.06        20.38        22.82        42.87        11.24        15.91 
TCGA-Z6-A8JE 
        2.10 

$`18Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30        58.55         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69         6.21        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
       14.50        12.16       122.10        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       24.03         6.28         3.16         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
        0.10        13.15        15.35         0.10        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.00        12.23        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        1.45        12.69         7.00        20.02         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        4.80        15.35         9.27         4.44        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD 
       18.18        46.19        15.06         9.17        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               0.1                0.1 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             60.39             122.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             12.03              12.59 
[1] "0.1 - 60.4 (12.0)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.4"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         2        1        1        0         3         3
  18Q GAIN WILD-TYPE       6        4        6        1        36        26
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED          10          2          1          0        1
  18Q GAIN WILD-TYPE        15         10          9          7        4
                    vv
clus                 STAGE IVA
  18Q GAIN MUTATED           0
  18Q GAIN WILD-TYPE         4
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  4
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 3                 36
  STAGE IIB                 3                 26
  STAGE III                10                 15
  STAGE IIIA                2                 10
  STAGE IIIB                1                  9
  STAGE IIIC                0                  7
  STAGE IV                  1                  4
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18Q GAIN MUTATED       5  4 15  1
  18Q GAIN WILD-TYPE    26 32 70  4
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                5                 26
  T2                   4                 32
  T3                  15                 70
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18Q GAIN MUTATED    9 14  1  1
  18Q GAIN WILD-TYPE 62 50 11  7
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                9                 62
  N1               14                 50
  N2                1                 11
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    21   1
  18Q GAIN WILD-TYPE 105   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     21    1
  18Q GAIN WILD-TYPE  105    8
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               21                105
  1                1                  8
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3  23
  18Q GAIN WILD-TYPE  21 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3   23
  18Q GAIN WILD-TYPE   21  126
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                 21
  MALE                 23                126
[1] 2 2
[1] FALSE
D33V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       5                         0    16
  18Q GAIN WILD-TYPE    36                         2    95
D33V9, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    5                 36
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   16                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    0  9
  18Q GAIN WILD-TYPE  3 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    9
  18Q GAIN WILD-TYPE    3   72
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                9                 72
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   16 10
  19P GAIN WILD-TYPE 84 61
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                26                145 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                 61 
$`19P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-IG-A3QL TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OO 
       58.55         8.94        20.09         3.16        24.00         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A8NG TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K 
        1.38         3.16        35.97        27.12        10.36         5.92 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-R6-A6KZ 
       13.15         0.10        25.25        12.00         0.13         5.06 
TCGA-R6-A6XG TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EX 
       29.59        12.69        20.38        15.35        19.96        28.11 
TCGA-VR-AA7I TCGA-X8-AAAR 
       15.91        10.16 

$`19P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       16.24         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF 
        6.28        30.25         0.30         4.31         8.94         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L 
        8.71        13.41        83.24        52.57        46.09        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       12.66        12.43        13.41         0.10        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.23        12.03        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       33.11         5.16         7.82         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        1.45         7.00        20.02         5.29         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        18.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.06        11.24         9.17         3.42         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               0.1                0.1 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             58.55             122.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             12.92              12.49 
[1] "0.1 - 58.5 (12.9)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         1        1        1        0         6         3
  19P GAIN WILD-TYPE       7        4        6        1        33        26
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           3          1          2          2        0
  19P GAIN WILD-TYPE        22         11          8          5        5
                    vv
clus                 STAGE IVA
  19P GAIN MUTATED           1
  19P GAIN WILD-TYPE         3
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  4
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 6                 33
  STAGE IIB                 3                 26
  STAGE III                 3                 22
  STAGE IIIA                1                 11
  STAGE IIIB                2                  8
  STAGE IIIC                2                  5
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  19P GAIN MUTATED       4  5 12  1
  19P GAIN WILD-TYPE    27 31 73  4
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                4                 27
  T2                   5                 31
  T3                  12                 73
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19P GAIN MUTATED   13  4  3  2
  19P GAIN WILD-TYPE 58 60  9  6
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               13                 58
  N1                4                 60
  N2                3                  9
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    14   1
  19P GAIN WILD-TYPE 112   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     14    1
  19P GAIN WILD-TYPE  112    8
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               14                112
  1                1                  8
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  26
  19P GAIN WILD-TYPE  24 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   26
  19P GAIN WILD-TYPE   24  123
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                0                 24
  MALE                 26                123
[1] 2 2
[1] FALSE
D34V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       6                         1    16
  19P GAIN WILD-TYPE    35                         1    95
D34V9, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    6                 35
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   16                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1 13
  19P GAIN WILD-TYPE  2 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   13
  19P GAIN WILD-TYPE    2   68
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               13                 68
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   22 15
  19Q GAIN WILD-TYPE 78 56
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                37                134 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                15                 56 
$`19Q GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A4QS 
       58.55         7.63         8.94        16.24        20.09         3.88 
TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OQ 
        3.16        24.00         3.68        32.61         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV 
        3.16        35.97        13.55         5.49        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A4A6 TCGA-LN-A5U7 
       46.09        10.36         5.92        15.35         0.10        25.25 
TCGA-LN-A7HW TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8WG 
       12.00         0.13         5.06        14.70        29.59        12.69 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR 
       20.38        15.35        19.96        28.11        15.91        10.16 
TCGA-Z6-A8JE 
        2.10 

$`19Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       25.78        31.27        14.30         5.92        13.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69         6.21        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.50        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31         8.94         4.70        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         7.17        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.95         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       13.41        83.24        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.10        13.15         0.10        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV 
       11.54        12.33        13.22         4.47        12.33        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.23        12.03        13.18        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         7.59         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89         1.45         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        3.42         4.80         9.27         4.44        18.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       42.87        46.19        15.06        11.24         9.17         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               0.1                0.1 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             58.55             122.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            13.550             12.475 
[1] "0.1 - 58.5 (13.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         2        1        2        1         7         4
  19Q GAIN WILD-TYPE       6        4        5        0        32        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           5          2          3          2        0
  19Q GAIN WILD-TYPE        20         10          7          5        5
                    vv
clus                 STAGE IVA
  19Q GAIN MUTATED           2
  19Q GAIN WILD-TYPE         2
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  4
  STAGE IB                  2                  5
  STAGE II                  1                  0
  STAGE IIA                 7                 32
  STAGE IIB                 4                 25
  STAGE III                 5                 20
  STAGE IIIA                2                 10
  STAGE IIIB                3                  7
  STAGE IIIC                2                  5
  STAGE IV                  0                  5
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  19Q GAIN MUTATED       6  7 18  1
  19Q GAIN WILD-TYPE    25 29 67  4
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                6                 25
  T2                   7                 29
  T3                  18                 67
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19Q GAIN MUTATED   16 10  4  2
  19Q GAIN WILD-TYPE 55 54  8  6
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               16                 55
  N1               10                 54
  N2                4                  8
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    22   2
  19Q GAIN WILD-TYPE 104   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     22    2
  19Q GAIN WILD-TYPE  104    7
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               22                104
  1                2                  7
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  36
  19Q GAIN WILD-TYPE  23 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   36
  19Q GAIN WILD-TYPE   23  113
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                 23
  MALE                 36                113
[1] 2 2
[1] FALSE
D35V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       6                         1    25
  19Q GAIN WILD-TYPE    35                         1    86
D35V9, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    6                 35
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   25                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1 16
  19Q GAIN WILD-TYPE  2 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   16
  19Q GAIN WILD-TYPE    2   65
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               16                 65
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   54 47
  20P GAIN WILD-TYPE 46 24
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               101                 70 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                47                 24 
$`20P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        20.09         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        2.63        20.12         3.88         0.53        17.03        23.41 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A939 
        4.67        14.50        12.16       122.10         3.68        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        25.22         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        4.31        24.00         4.70        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF 
        6.94         2.60         0.36         7.40        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       35.97        12.92        16.47         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R 
       27.12        52.57        46.09        10.36        10.45         0.10 
TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A9 
       13.15         0.10        12.49        12.76         0.10        11.54 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN 
       12.33        25.25        12.23        13.18         0.13         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06        14.70         7.04         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89        12.69        20.02         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW 
        4.80         9.27         4.44        19.96         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
       28.11        30.71        18.18        42.87        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91         2.10         2.66        19.73 

$`20P GAIN WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A4P3 
       14.30        58.55         7.63         6.21        20.78        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA 
        9.30         0.79        12.82         9.96        14.86        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F 
       60.39        68.02        41.52        42.77        25.41        24.03 
TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        6.28         8.94         3.68        32.61        19.99        21.01 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 
        3.32         3.16         8.71        25.12         3.95         3.02 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.48        13.55        13.22         7.76        21.37        83.24 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V 
        5.92        12.66        12.43        13.41        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       13.25        12.46        12.59        12.59        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       12.33        13.22         4.47        10.52        12.00        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WC 
       33.11         5.16         7.82        29.59        53.95         1.45 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
        7.00        20.38        15.35        18.81        22.82        12.43 
TCGA-VR-A8EU TCGA-VR-AA4G TCGA-X8-AAAR TCGA-Z6-A8JD 
       18.31        15.06        10.16         3.42 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               0.1                0.1 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            122.10              83.24 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             11.54              13.22 
[1] "0.1 - 122.1 (11.5)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.6"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         3        2        4        1        20        16
  20P GAIN WILD-TYPE       5        3        3        0        19        13
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED          14          9          6          5        3
  20P GAIN WILD-TYPE        11          3          4          2        2
                    vv
clus                 STAGE IVA
  20P GAIN MUTATED           4
  20P GAIN WILD-TYPE         0
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  2                  3
  STAGE IB                  4                  3
  STAGE II                  1                  0
  STAGE IIA                20                 19
  STAGE IIB                16                 13
  STAGE III                14                 11
  STAGE IIIA                9                  3
  STAGE IIIB                6                  4
  STAGE IIIC                5                  2
  STAGE IV                  3                  2
  STAGE IVA                 4                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20P GAIN MUTATED      19 17 51  2
  20P GAIN WILD-TYPE    12 19 34  3
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               19                 12
  T2                  17                 19
  T3                  51                 34
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20P GAIN MUTATED   36 39  7  6
  20P GAIN WILD-TYPE 35 25  5  2
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               36                 35
  N1               39                 25
  N2                7                  5
  N3                6                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   69  7
  20P GAIN WILD-TYPE 57  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     69    7
  20P GAIN WILD-TYPE   57    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               69                 57
  1                7                  2
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   12 90
  20P GAIN WILD-TYPE 12 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12   90
  20P GAIN WILD-TYPE   12   59
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               12                 12
  MALE                 90                 59
[1] 2 2
[1] FALSE
D36V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED      19                         1    69
  20P GAIN WILD-TYPE    22                         1    42
D36V9, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                   19                 22
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   69                 42
[1] 3 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, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    3 44
  20P GAIN WILD-TYPE  0 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   44
  20P GAIN WILD-TYPE    0   37
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO               44                 37
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   59 50
  20Q GAIN WILD-TYPE 41 21
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               109                 62 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                50                 21 
$`20Q GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63        20.12         3.88         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE 
       23.41         4.67        14.50        12.16       122.10         3.68 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        31.56        25.22         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31        24.00         3.68         4.70        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40        55.50         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R 
       27.12        52.57        46.09        10.36        10.45         0.10 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.15         0.10         0.10        12.49        12.76         0.10 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       12.33        25.25        12.23        12.03        13.18         0.13 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.02         5.29         3.42         4.80         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
        4.44        19.96         1.55         8.12        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JE TCGA-Z6-AAPN 
       42.87        46.19        11.24         9.17         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`20Q GAIN WILD-TYPE`
TCGA-2H-A9GL TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT 
        5.92         6.21        20.09        20.78        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB 
        0.79        12.82         9.96        14.86        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC 
       68.02        41.52        42.77        25.41        24.03         6.28 
TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A88T TCGA-L5-A88W 
        8.94        19.99        21.01         3.32         8.71        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NU 
        3.95         3.02        13.48        13.55         7.76        83.24 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W 
        5.92        12.66        12.43        13.41        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.59        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-M9-A5M8 
       12.33        13.22         4.47        10.52        12.00        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO 
        5.16         7.82         1.45        20.38        15.35        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I 
       22.82        12.43        18.31        30.71        15.06        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD 
       10.16         3.42 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.10               0.79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            122.10              83.24 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            12.030             13.235 
[1] "0.1 - 122.1 (12.0)" "0.8 - 83.2 (13.2)" 
[1] "hr=" "1.5"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         5        3        4        1        20        17
  20Q GAIN WILD-TYPE       3        2        3        0        19        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED          16          9          6          5        3
  20Q GAIN WILD-TYPE         9          3          4          2        2
                    vv
clus                 STAGE IVA
  20Q GAIN MUTATED           4
  20Q GAIN WILD-TYPE         0
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   5                  3
  STAGE IA                  3                  2
  STAGE IB                  4                  3
  STAGE II                  1                  0
  STAGE IIA                20                 19
  STAGE IIB                17                 12
  STAGE III                16                  9
  STAGE IIIA                9                  3
  STAGE IIIB                6                  4
  STAGE IIIC                5                  2
  STAGE IV                  3                  2
  STAGE IVA                 4                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20Q GAIN MUTATED      24 17 53  1
  20Q GAIN WILD-TYPE     7 19 32  4
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               24                  7
  T2                  17                 19
  T3                  53                 32
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   37 44  7  6
  20Q GAIN WILD-TYPE 34 20  5  2
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               37                 34
  N1               44                 20
  N2                7                  5
  N3                6                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   73  7
  20Q GAIN WILD-TYPE 53  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     73    7
  20Q GAIN WILD-TYPE   53    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               73                 53
  1                7                  2
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   12 98
  20Q GAIN WILD-TYPE 12 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     12   98
  20Q GAIN WILD-TYPE   12   51
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               12                 12
  MALE                 98                 51
[1] 2 2
[1] FALSE
D37V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED      20                         1    74
  20Q GAIN WILD-TYPE    21                         1    37
D37V9, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                   20                 21
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   74                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    3 47
  20Q GAIN WILD-TYPE  0 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   47
  20Q GAIN WILD-TYPE    0   34
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO               47                 34
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   13  3
  21Q GAIN WILD-TYPE 87 68
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                16                155 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 68 
$`21Q GAIN MUTATED`
TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A93E TCGA-L5-A4OF 
        2.63        23.41         4.67        14.50        25.22         3.68 
TCGA-L5-A8NE TCGA-L5-A8NN TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 
       55.50         5.49        10.45        15.35         0.10        12.59 
TCGA-S8-A6BV TCGA-V5-A7RC TCGA-VR-A8EP TCGA-X8-AAAR 
       20.02         3.42        19.96        10.16 

$`21Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        6.21        33.27        20.09         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82         9.96        14.86        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       30.25         0.30         4.31         8.94        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.95         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36         5.92        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.10        13.15        13.25         0.10        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       12.00        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         1.45        12.69         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        18.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91         3.42         2.10         2.66        19.73 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               0.1                0.1 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              55.5              122.1 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             11.52              12.59 
[1] "0.1 - 55.5 (11.5)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "2"  
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         0        0        0        0         5         3
  21Q GAIN WILD-TYPE       8        5        7        1        34        26
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           1          3          2          0        0
  21Q GAIN WILD-TYPE        24          9          8          7        5
                    vv
clus                 STAGE IVA
  21Q GAIN MUTATED           0
  21Q GAIN WILD-TYPE         4
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  0                  7
  STAGE II                  0                  1
  STAGE IIA                 5                 34
  STAGE IIB                 3                 26
  STAGE III                 1                 24
  STAGE IIIA                3                  9
  STAGE IIIB                2                  8
  STAGE IIIC                0                  7
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  21Q GAIN MUTATED       2  2 11  0
  21Q GAIN WILD-TYPE    29 34 74  5
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                2                 29
  T2                   2                 34
  T3                  11                 74
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  21Q GAIN MUTATED    5  7  2  0
  21Q GAIN WILD-TYPE 66 57 10  8
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                5                 66
  N1                7                 57
  N2                2                 10
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    12   0
  21Q GAIN WILD-TYPE 114   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     12    0
  21Q GAIN WILD-TYPE  114    9
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               12                114
  1                0                  9
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  15
  21Q GAIN WILD-TYPE  23 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   15
  21Q GAIN WILD-TYPE   23  134
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                1                 23
  MALE                 15                134
[1] 2 2
[1] FALSE
D38V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       6                         1     9
  21Q GAIN WILD-TYPE    35                         1   102
D38V9, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    6                 35
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    9                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    0 11
  21Q GAIN WILD-TYPE  3 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   11
  21Q GAIN WILD-TYPE    3   70
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               11                 70
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   18 10
  22Q GAIN WILD-TYPE 82 61
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                28                143 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                 61 
$`22Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A97H TCGA-L5-A43E TCGA-L5-A43J 
       20.09         0.85        20.78        14.50        30.25         4.31 
TCGA-L5-A4OM TCGA-L5-A8NT TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 
       47.93        27.12        12.59        12.49        12.59         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX 
       11.54        12.33        13.22        12.33        12.00        12.23 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP 
        0.13         5.16        12.69        20.38         3.42        19.96 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B 
        8.12        28.11        18.18        11.24 

$`22Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        6.21        33.27         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         0.30         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A5U5 
        0.10        12.46        12.76        22.39        15.52         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       25.25        10.52        12.03        13.18        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         1.45 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.02         5.29         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        22.82        12.43         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       30.71        42.87        46.19        15.06         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       10.16         3.42         2.10         2.66        19.73 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               0.1                0.1 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             47.93             122.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             12.54              12.66 
[1] "0.1 - 47.9 (12.5)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1"  
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1        1        1        1         9         4
  22Q GAIN WILD-TYPE       7        4        6        0        30        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           2          2          3          1        1
  22Q GAIN WILD-TYPE        23         10          7          6        4
                    vv
clus                 STAGE IVA
  22Q GAIN MUTATED           1
  22Q GAIN WILD-TYPE         3
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  4
  STAGE IB                  1                  6
  STAGE II                  1                  0
  STAGE IIA                 9                 30
  STAGE IIB                 4                 25
  STAGE III                 2                 23
  STAGE IIIA                2                 10
  STAGE IIIB                3                  7
  STAGE IIIC                1                  6
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  22Q GAIN MUTATED       3  8 14  2
  22Q GAIN WILD-TYPE    28 28 71  3
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1                3                 28
  T2                   8                 28
  T3                  14                 71
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  22Q GAIN MUTATED   17  4  3  2
  22Q GAIN WILD-TYPE 54 60  9  6
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               17                 54
  N1                4                 60
  N2                3                  9
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    22   2
  22Q GAIN WILD-TYPE 104   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     22    2
  22Q GAIN WILD-TYPE  104    7
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               22                104
  1                2                  7
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  26
  22Q GAIN WILD-TYPE  21 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   26
  22Q GAIN WILD-TYPE   21  123
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                3                 21
  MALE                 26                123
[1] 2 2
[1] FALSE
D39V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED      14                         1    13
  22Q GAIN WILD-TYPE    27                         1    98
D39V9, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                   14                 27
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   13                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    1 19
  22Q GAIN WILD-TYPE  2 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   19
  22Q GAIN WILD-TYPE    2   62
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               19                 62
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED   12  9
  XP GAIN WILD-TYPE 88 62
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               21               150 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                9                62 
$`XP GAIN MUTATED`
TCGA-IG-A51D TCGA-JY-A6F8 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OQ TCGA-L5-A4OR 
       17.03       122.10         4.31        19.99         1.38         3.16 
TCGA-L5-A88Y TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A2 
        0.36         5.49        21.37        13.15         0.10        12.49 
TCGA-LN-A4A4 TCGA-LN-A7HZ TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EY 
       12.59        13.18         2.89         3.42        15.35        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-ZR-A9CJ 
       18.18        46.19        19.73 

$`XP GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.00         3.68         4.70        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         7.17        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
        0.10        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.23        12.03         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.02        20.38         5.29         4.80         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        4.44        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       18.31         8.12        28.11        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91        10.16         3.42         2.10         2.66 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
              0.1               0.1 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           122.10             83.24 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           13.150            12.445 
[1] "0.1 - 122.1 (13.2)" "0.1 - 83.2 (12.4)" 
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         1        1        1        0         6         3
  XP GAIN WILD-TYPE       7        4        6        1        33        26
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           2          1          0          3        0
  XP GAIN WILD-TYPE        23         11         10          4        5
                   vv
clus                STAGE IVA
  XP GAIN MUTATED           0
  XP GAIN WILD-TYPE         4
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 1                 4
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA                6                33
  STAGE IIB                3                26
  STAGE III                2                23
  STAGE IIIA               1                11
  STAGE IIIB               0                10
  STAGE IIIC               3                 4
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  XP GAIN MUTATED       5  3 11  0
  XP GAIN WILD-TYPE    26 33 74  5
D40V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1               5                26
  T2                  3                33
  T3                 11                74
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  XP GAIN MUTATED   11  4  1  3
  XP GAIN WILD-TYPE 60 60 11  5
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              11                60
  N1               4                60
  N2               1                11
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    12   0
  XP GAIN WILD-TYPE 114   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     12    0
  XP GAIN WILD-TYPE  114    9
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              12               114
  1               0                 9
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1  20
  XP GAIN WILD-TYPE  23 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   20
  XP GAIN WILD-TYPE   23  129
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               1                23
  MALE                20               129
[1] 2 2
[1] FALSE
D40V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       5                         2    14
  XP GAIN WILD-TYPE    36                         0    97
D40V9, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   5                36
  BLACK OR AFRICAN AMERICAN               2                 0
  WHITE                                  14                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"
D40V10, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    0 10
  XP GAIN WILD-TYPE  3 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   10
  XP GAIN WILD-TYPE    3   71
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              10                71
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   19 15
  XQ GAIN WILD-TYPE 81 56
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34               137 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               15                56 
$`XQ GAIN MUTATED`
TCGA-2H-A9GI TCGA-IG-A3QL TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       14.30        20.09         3.88         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A43J 
        9.96         4.67       122.10        44.75        23.18         4.31 
TCGA-L5-A4OI TCGA-L5-A4OQ TCGA-L5-A88Y TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49K 
       19.99         1.38         0.36         5.49        21.37         5.92 
TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       12.66         0.10         0.10        12.59        12.49        12.59 
TCGA-LN-A7HZ TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW 
       13.18         2.89        20.02        15.35        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-ZR-A9CJ 
       30.71        18.18        46.19        19.73 

$`XQ GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        9.30         0.79        12.82        14.86        14.50        12.16 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        6.94         8.71         2.60        25.12         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22         7.76         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       27.12        83.24        52.57        46.09        10.36        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41         0.10        13.15        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.76        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.00        12.23        12.03         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
       29.59         6.35        53.95         9.30        15.78         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
        1.55        28.11        42.87        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.91        10.16         3.42         2.10         2.66 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              0.1               0.1 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           122.10             83.24 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            12.92             12.43 
[1] "0.1 - 122.1 (12.9)" "0.1 - 83.2 (12.4)" 
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         1        0        1        0         9         8
  XQ GAIN WILD-TYPE       7        5        6        1        30        21
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           3          3          4          3        1
  XQ GAIN WILD-TYPE        22          9          6          4        4
                   vv
clus                STAGE IVA
  XQ GAIN MUTATED           0
  XQ GAIN WILD-TYPE         4
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA                9                30
  STAGE IIB                8                21
  STAGE III                3                22
  STAGE IIIA               3                 9
  STAGE IIIB               4                 6
  STAGE IIIC               3                 4
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  XQ GAIN MUTATED       5  7 22  0
  XQ GAIN WILD-TYPE    26 29 63  5
D41V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               5                26
  T2                  7                29
  T3                 22                63
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  XQ GAIN MUTATED   15 11  5  3
  XQ GAIN WILD-TYPE 56 53  7  5
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              15                56
  N1              11                53
  N2               5                 7
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    26   1
  XQ GAIN WILD-TYPE 100   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     26    1
  XQ GAIN WILD-TYPE  100    8
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              26               100
  1               1                 8
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2  33
  XQ GAIN WILD-TYPE  22 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   33
  XQ GAIN WILD-TYPE   22  116
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               2                22
  MALE                33               116
[1] 2 2
[1] FALSE
D41V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED      14                         1    19
  XQ GAIN WILD-TYPE    27                         1    92
D41V9, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                  14                27
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  19                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    0 20
  XQ GAIN WILD-TYPE  3 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   20
  XQ GAIN WILD-TYPE    3   61
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              20                61
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   19 15
  1P LOSS WILD-TYPE 81 56
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               137 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15                56 
$`1P LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4P3 
       14.30         7.63        16.24        32.45        33.27        18.64 
TCGA-JY-A6FB TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        23.18         0.30         8.94        24.00         4.70 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG 
        4.90        29.00         2.60         7.40        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-R6-A6DN 
       12.92        16.47        25.25        12.00        13.18         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW 
        7.59         5.06         6.35         2.89         1.45        20.38 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER 
        4.80         9.27         4.44        12.43 

$`1P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21         7.69         6.21        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       41.52        42.77        25.41        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         4.31         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38         3.16        58.59         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        6.94         8.71        25.12         0.36         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO 
        4.47        12.33        10.52        12.23        12.03         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         5.16         7.82        14.70         7.04        29.59 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       53.95         9.30        15.78        12.69         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        5.29         3.42        15.35        18.81        19.96        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       10.16         3.42         2.10         2.66        19.73 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              0.3               0.1 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            60.39            122.10 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           12.215            12.590 
[1] "0.3 - 60.4 (12.2)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.1"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         2        0        2        0         7         2
  1P LOSS WILD-TYPE       6        5        5        1        32        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           7          0          2          0        2
  1P LOSS WILD-TYPE        18         12          8          7        3
                   vv
clus                STAGE IVA
  1P LOSS MUTATED           1
  1P LOSS WILD-TYPE         3
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 0                 5
  STAGE IB                 2                 5
  STAGE II                 0                 1
  STAGE IIA                7                32
  STAGE IIB                2                27
  STAGE III                7                18
  STAGE IIIA               0                12
  STAGE IIIB               2                 8
  STAGE IIIC               0                 7
  STAGE IV                 2                 3
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  1P LOSS MUTATED       5  6 14  1
  1P LOSS WILD-TYPE    26 30 71  4
D42V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               5                26
  T2                  6                30
  T3                 14                71
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  1P LOSS MUTATED   11 12  3  0
  1P LOSS WILD-TYPE 60 52  9  8
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              11                60
  N1              12                52
  N2               3                 9
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    19   3
  1P LOSS WILD-TYPE 107   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     19    3
  1P LOSS WILD-TYPE  107    6
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              19               107
  1               3                 6
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     5  29
  1P LOSS WILD-TYPE  19 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   29
  1P LOSS WILD-TYPE   19  120
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               5                19
  MALE                29               120
[1] 2 2
[1] FALSE
D42V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       4                         0    24
  1P LOSS WILD-TYPE    37                         2    87
D42V9, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   4                37
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  24                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"
D42V10, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    0 15
  1P LOSS WILD-TYPE  3 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   15
  1P LOSS WILD-TYPE    3   66
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15                66
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    9 11
  1Q LOSS WILD-TYPE 91 60
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               151 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               11                60 
$`1Q LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-L5-A43M TCGA-L5-A4OE 
        7.63        16.24        33.27         3.88         8.94        24.00 
TCGA-L5-A4OT TCGA-L5-A88V TCGA-LN-A49O TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ 
        4.90         2.60        13.41        25.25         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RE 
        5.06         6.35         2.89         1.45        20.38         4.80 
TCGA-V5-AASX TCGA-VR-A8ER 
        4.44        12.43 

$`1Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL 
        8.94         4.21        32.45         7.69         6.21        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16        30.25         0.30         4.31         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.43         6.94         8.71        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13        33.11         5.16         7.82        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO 
       29.59        53.95         9.30        15.78        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
       20.02         5.29         3.42        15.35         9.27        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91        10.16         3.42         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.45              0.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            33.27            122.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             7.61             12.76 
[1] "1.4 - 33.3 (7.6)"   "0.1 - 122.1 (12.8)"
[1] "hr=" "2.3"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        0        2        0         3         0
  1Q LOSS WILD-TYPE       8        5        5        1        36        29
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           3          0          2          0        1
  1Q LOSS WILD-TYPE        22         12          8          7        4
                   vv
clus                STAGE IVA
  1Q LOSS MUTATED           1
  1Q LOSS WILD-TYPE         3
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 5
  STAGE IB                 2                 5
  STAGE II                 0                 1
  STAGE IIA                3                36
  STAGE IIB                0                29
  STAGE III                3                22
  STAGE IIIA               0                12
  STAGE IIIB               2                 8
  STAGE IIIC               0                 7
  STAGE IV                 1                 4
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  1Q LOSS MUTATED       1  2  9  1
  1Q LOSS WILD-TYPE    30 34 76  4
D43V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               1                30
  T2                  2                34
  T3                  9                76
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  1Q LOSS MUTATED    5  5  3  0
  1Q LOSS WILD-TYPE 66 59  9  8
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               5                66
  N1               5                59
  N2               3                 9
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     7   2
  1Q LOSS WILD-TYPE 119   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7    2
  1Q LOSS WILD-TYPE  119    7
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               7               119
  1               2                 7
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  17
  1Q LOSS WILD-TYPE  21 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   17
  1Q LOSS WILD-TYPE   21  132
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3                21
  MALE                17               132
[1] 2 2
[1] FALSE
D43V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         0    14
  1Q LOSS WILD-TYPE    39                         2    97
D43V9, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                39
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  14                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"
D43V10, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    0 13
  1Q LOSS WILD-TYPE  3 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   13
  1Q LOSS WILD-TYPE    3   68
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              13                68
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED   10  1
  2P LOSS WILD-TYPE 90 70
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               160 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                70 
$`2P LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-L5-A4OS TCGA-L5-A8NE TCGA-L5-A8NK TCGA-LN-A7HV 
        2.63        20.12        58.59        55.50        13.55        10.52 
TCGA-LN-A7HX TCGA-R6-A8W8 TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-AAPN 
       12.23         2.89        18.81        42.87         2.66 

$`2P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
        6.21        33.27        20.09         0.85        20.78        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35         0.10        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.00        12.03        13.18         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
       29.59         6.35        53.95         9.30        15.78         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       12.69         7.00        20.02        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       10.16         3.42         2.10        19.73 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.63              0.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            58.59            122.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            13.55             12.54 
[1] "2.6 - 58.6 (13.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "6.6"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        0        0         4         2
  2P LOSS WILD-TYPE       8        5        7        1        35        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           0          3          1          0        0
  2P LOSS WILD-TYPE        25          9          9          7        5
                   vv
clus                STAGE IVA
  2P LOSS MUTATED           0
  2P LOSS WILD-TYPE         4
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 5
  STAGE IB                 0                 7
  STAGE II                 0                 1
  STAGE IIA                4                35
  STAGE IIB                2                27
  STAGE III                0                25
  STAGE IIIA               3                 9
  STAGE IIIB               1                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  2P LOSS MUTATED       0  4  6  0
  2P LOSS WILD-TYPE    31 32 79  5
D44V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               0                31
  T2                  4                32
  T3                  6                79
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  2P LOSS MUTATED    5  5  0  0
  2P LOSS WILD-TYPE 66 59 12  8
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               5                66
  N1               5                59
  N2               0                12
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    10   0
  2P LOSS WILD-TYPE 116   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10    0
  2P LOSS WILD-TYPE  116    9
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              10               116
  1               0                 9
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2   9
  2P LOSS WILD-TYPE  22 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    9
  2P LOSS WILD-TYPE   22  140
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                22
  MALE                 9               140
[1] 2 2
[1] FALSE
D44V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       2                         0     9
  2P LOSS WILD-TYPE    39                         2   102
D44V9, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   2                39
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   9               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    0  6
  2P LOSS WILD-TYPE  3 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    6
  2P LOSS WILD-TYPE    3   75
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               6                75
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED   13  5
  2Q LOSS WILD-TYPE 87 66
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               153 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                66 
$`2Q LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A43H TCGA-L5-A4OS 
        2.63        20.12        18.64         0.79         0.30        58.59 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ 
        3.02        16.47        13.55        10.45        12.46        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-R6-A8W8 TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-AAPN 
       10.52        12.23         2.89        18.81        42.87         2.66 

$`2Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS 
        6.21        33.27        20.09         0.85        20.78         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16        30.25         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.95        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.48        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36         5.92        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35         0.10        13.25         0.10        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         4.44        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        3.42         2.10        19.73 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              0.3               0.1 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            58.59            122.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            12.28             12.66 
[1] "0.3 - 58.6 (12.3)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         1        0        1        0         6         2
  2Q LOSS WILD-TYPE       7        5        6        1        33        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           3          3          1          0        0
  2Q LOSS WILD-TYPE        22          9          9          7        5
                   vv
clus                STAGE IVA
  2Q LOSS MUTATED           0
  2Q LOSS WILD-TYPE         4
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 5
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA                6                33
  STAGE IIB                2                27
  STAGE III                3                22
  STAGE IIIA               3                 9
  STAGE IIIB               1                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  2Q LOSS MUTATED       1  5 11  0
  2Q LOSS WILD-TYPE    30 31 74  5
D45V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               1                30
  T2                  5                31
  T3                 11                74
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  2Q LOSS MUTATED    9  8  0  0
  2Q LOSS WILD-TYPE 62 56 12  8
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               9                62
  N1               8                56
  N2               0                12
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    17   0
  2Q LOSS WILD-TYPE 109   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17    0
  2Q LOSS WILD-TYPE  109    9
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              17               109
  1               0                 9
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     3  15
  2Q LOSS WILD-TYPE  21 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   15
  2Q LOSS WILD-TYPE   21  134
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               3                21
  MALE                15               134
[1] 2 2
[1] FALSE
D45V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       5                         0    13
  2Q LOSS WILD-TYPE    36                         2    98
D45V9, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   5                36
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  13                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    0 11
  2Q LOSS WILD-TYPE  3 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   11
  2Q LOSS WILD-TYPE    3   70
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              11                70
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   59 25
  3P LOSS WILD-TYPE 41 46
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               84                87 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               25                46 
$`3P LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       14.30        13.94         4.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63        20.12         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
        0.79        23.41         9.96        14.50        12.16        68.02 
TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
       25.41        30.25         8.94         4.70        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.32         7.17         7.13         7.43         6.94         2.60 
TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         2.66        35.97        12.92        16.47        13.55 
TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       13.41         5.92        12.43        13.41        13.15        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-RE-A7BO 
        0.13        33.11         7.59         7.04         6.35         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EU 
       20.02        20.38         3.42        18.81        19.96        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91        10.16         3.42         2.10         2.66 

$`3P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A4P3 TCGA-IG-A4QT 
       16.24        32.45         7.69         6.21        18.64         9.30 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82        14.86         4.67       122.10        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        42.77        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
       25.22        24.03         6.28         3.16         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
       24.00         3.68        19.99        47.93        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W 
        3.16        58.59         4.90        29.00         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL 
        0.36         3.95         3.02        55.50        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       52.57        46.09        10.36        10.45        12.66         0.10 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A9 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10        13.25        12.59        11.54         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         5.06        14.70        29.59        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RE 
       15.78         2.89         1.45        12.69         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         9.27         4.44        22.82        12.43         1.55 
TCGA-VR-A8EX TCGA-VR-AA7B TCGA-ZR-A9CJ 
       28.11        11.24        19.73 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              0.1               0.1 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            68.02            122.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           12.475            12.660 
[1] "0.1 - 68.0 (12.5)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.3"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         4        1        4        1        26        14
  3P LOSS WILD-TYPE       4        4        3        0        13        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED          10          9          4          3        3
  3P LOSS WILD-TYPE        15          3          6          4        2
                   vv
clus                STAGE IVA
  3P LOSS MUTATED           1
  3P LOSS WILD-TYPE         3
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  4                 4
  STAGE IA                 1                 4
  STAGE IB                 4                 3
  STAGE II                 1                 0
  STAGE IIA               26                13
  STAGE IIB               14                15
  STAGE III               10                15
  STAGE IIIA               9                 3
  STAGE IIIB               4                 6
  STAGE IIIC               3                 4
  STAGE IV                 3                 2
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3P LOSS MUTATED      14 19 46  3
  3P LOSS WILD-TYPE    17 17 39  2
D46V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              14                17
  T2                 19                17
  T3                 46                39
  T4                  3                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3P LOSS MUTATED   44 29  5  3
  3P LOSS WILD-TYPE 27 35  7  5
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              44                27
  N1              29                35
  N2               5                 7
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   71  4
  3P LOSS WILD-TYPE 55  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     71    4
  3P LOSS WILD-TYPE   55    5
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              71                55
  1               4                 5
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   14 72
  3P LOSS WILD-TYPE 10 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     14   72
  3P LOSS WILD-TYPE   10   77
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              14                10
  MALE                72                77
[1] 2 2
[1] FALSE
D46V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED      30                         1    48
  3P LOSS WILD-TYPE    11                         1    63
D46V9, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                  30                11
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  48                63
[1] 3 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, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    0 51
  3P LOSS WILD-TYPE  3 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   51
  3P LOSS WILD-TYPE    3   30
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              51                30
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   18 12
  3Q LOSS WILD-TYPE 82 59
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               30               141 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12                59 
$`3Q LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YA TCGA-IG-A5S3 
       14.30        13.94         4.21        32.45        20.78        23.41 
TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Z 
       25.41        30.25        32.61         3.32         7.43         7.40 
TCGA-L5-A8NH TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U5 
       12.92         5.92        15.35        12.46         0.10         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A9FO TCGA-R6-A6XQ TCGA-RE-A7BO 
       12.33        25.25        12.23         0.13         6.35         7.00 
TCGA-VR-A8EP TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       19.96        18.18        46.19        10.16         3.42         2.10 

$`3Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.50        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        42.77        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
       25.22        24.03         6.28         3.16         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94        24.00         3.68         4.70        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         0.36         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        5.49        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41         0.10        13.15         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       11.54        12.33        13.22        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        14.70         7.04        29.59        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         2.89         1.45        12.69        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        30.71        42.87        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91         2.66        19.73 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              0.1               0.1 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            46.19            122.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           12.395            12.590 
[1] "0.1 - 46.2 (12.4)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        0        1        1         9         8
  3Q LOSS WILD-TYPE       6        5        6        0        30        21
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           2          2          1          2        2
  3Q LOSS WILD-TYPE        23         10          9          5        3
                   vv
clus                STAGE IVA
  3Q LOSS MUTATED           0
  3Q LOSS WILD-TYPE         4
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 0                 5
  STAGE IB                 1                 6
  STAGE II                 1                 0
  STAGE IIA                9                30
  STAGE IIB                8                21
  STAGE III                2                23
  STAGE IIIA               2                10
  STAGE IIIB               1                 9
  STAGE IIIC               2                 5
  STAGE IV                 2                 3
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3Q LOSS MUTATED       8  7 15  1
  3Q LOSS WILD-TYPE    23 29 70  4
D47V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1               8                23
  T2                  7                29
  T3                 15                70
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3Q LOSS MUTATED   16 12  1  2
  3Q LOSS WILD-TYPE 55 52 11  6
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              16                55
  N1              12                52
  N2               1                11
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   28  2
  3Q LOSS WILD-TYPE 98  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     28    2
  3Q LOSS WILD-TYPE   98    7
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              28                98
  1               2                 7
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3  29
  3Q LOSS WILD-TYPE  21 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3   29
  3Q LOSS WILD-TYPE   21  120
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               3                21
  MALE                29               120
[1] 2 2
[1] FALSE
D47V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED      11                         0    17
  3Q LOSS WILD-TYPE    30                         2    94
D47V9, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                  11                30
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  17                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    0 18
  3Q LOSS WILD-TYPE  3 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   18
  3Q LOSS WILD-TYPE    3   63
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              18                63
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   54 44
  4P LOSS WILD-TYPE 46 27
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               98                73 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               44                27 
$`4P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.78        20.12        18.64         3.88         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82         9.96         4.67        12.16        44.75        60.39 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE 
       42.77        23.18        25.22         3.16         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        4.70        21.01         3.16         4.90         7.13         7.43 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         3.95        35.97        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.22         8.71        13.41        27.12        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U 
        5.92        10.45        12.66        12.43         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.25         0.10        12.59        12.49        12.76         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.00        12.23        13.18         0.13         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        5.06         7.04         6.35         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.38         3.42         4.80         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7I TCGA-Z6-A8JD 
       15.91         3.42 

$`4P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YB TCGA-IG-A4QT 
       31.27         7.63         7.69         6.21         2.63         9.30 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD 
       17.03        23.41        14.86        14.50       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
        3.68        41.52        25.41        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28        30.25         0.30         4.31         3.68        32.61 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       58.59        29.00         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM 
        0.36         3.02        55.50         2.66        13.48         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49O TCGA-LN-A49S 
        5.49        21.37        83.24        52.57        13.41        13.15 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A5U5 
        0.10        12.46        12.59        22.39        11.54         4.47 
TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG 
       12.03        33.11         5.16         7.82        14.70        29.59 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV 
       53.95         9.30        15.78        20.02         5.29        15.35 
TCGA-VR-A8EO TCGA-VR-A8EY TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN 
       18.81        30.71         9.17        10.16         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              0.1               0.1 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            60.39            122.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            12.43             13.41 
[1] "0.1 - 60.4 (12.4)"  "0.1 - 122.1 (13.4)"
[1] "hr=" "1.6"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         4        1        5        1        21        15
  4P LOSS WILD-TYPE       4        4        2        0        18        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED          16          7          7          2        4
  4P LOSS WILD-TYPE         9          5          3          5        1
                   vv
clus                STAGE IVA
  4P LOSS MUTATED           2
  4P LOSS WILD-TYPE         2
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  4                 4
  STAGE IA                 1                 4
  STAGE IB                 5                 2
  STAGE II                 1                 0
  STAGE IIA               21                18
  STAGE IIB               15                14
  STAGE III               16                 9
  STAGE IIIA               7                 5
  STAGE IIIB               7                 3
  STAGE IIIC               2                 5
  STAGE IV                 4                 1
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  4P LOSS MUTATED      13 25 45  4
  4P LOSS WILD-TYPE    18 11 40  1
D48V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              13                18
  T2                 25                11
  T3                 45                40
  T4                  4                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4P LOSS MUTATED   37 38  9  3
  4P LOSS WILD-TYPE 34 26  3  5
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              37                34
  N1              38                26
  N2               9                 3
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   76  6
  4P LOSS WILD-TYPE 50  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     76    6
  4P LOSS WILD-TYPE   50    3
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              76                50
  1               6                 3
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   12 87
  4P LOSS WILD-TYPE 12 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     12   87
  4P LOSS WILD-TYPE   12   62
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              12                12
  MALE                87                62
[1] 2 2
[1] FALSE
D48V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED      29                         1    55
  4P LOSS WILD-TYPE    12                         1    56
D48V9, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                  29                12
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  55                56
[1] 3 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, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    1 50
  4P LOSS WILD-TYPE  2 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   50
  4P LOSS WILD-TYPE    2   31
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              50                31
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   43 41
  4Q LOSS WILD-TYPE 57 30
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               84                87 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               41                30 
$`4Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FA 
        3.88         0.53         0.79        12.82         4.67        44.75 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J 
       60.39        42.77        23.18        25.22         3.16         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
        8.94        24.00         4.70         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH 
        7.43         6.94         7.40         3.95        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       16.47        13.22         8.71        13.41        27.12        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       46.09        10.36         5.92        10.45        12.66         0.10 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       15.35        13.25        12.59        12.76         0.10        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
       13.18         8.02         7.59         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30         2.89         1.45        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       20.38         4.80         9.27         4.44        19.96        22.82 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I 
        1.55        28.11        18.18        42.87        11.24        15.91 

$`4Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YB 
       31.27         7.63         7.69         6.21        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12        18.64         9.30        17.03        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86        14.50        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        25.41        21.70        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       30.25         0.30         3.68        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 
       29.00         8.71         2.60        25.12         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       55.50         2.66        13.48        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V 
       21.37        52.57        12.43        13.41        13.15         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10        12.46        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       11.54        13.22        12.03         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB 
        7.82        14.70        53.95        15.78        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        3.42        15.35        18.81        12.43        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD 
       30.71        46.19        15.06         9.17        10.16         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         2.66        19.73 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              0.1               0.1 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            83.24            122.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           12.115            13.410 
[1] "0.1 - 83.2 (12.1)"  "0.1 - 122.1 (13.4)"
[1] "hr=" "1.7"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         3        1        5        1        15        12
  4Q LOSS WILD-TYPE       5        4        2        0        24        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED          15          4          6          2        4
  4Q LOSS WILD-TYPE        10          8          4          5        1
                   vv
clus                STAGE IVA
  4Q LOSS MUTATED           2
  4Q LOSS WILD-TYPE         2
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 1                 4
  STAGE IB                 5                 2
  STAGE II                 1                 0
  STAGE IIA               15                24
  STAGE IIB               12                17
  STAGE III               15                10
  STAGE IIIA               4                 8
  STAGE IIIB               6                 4
  STAGE IIIC               2                 5
  STAGE IV                 4                 1
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  4Q LOSS MUTATED      10 18 42  2
  4Q LOSS WILD-TYPE    21 18 43  3
D49V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              10                21
  T2                 18                18
  T3                 42                43
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4Q LOSS MUTATED   30 32  7  3
  4Q LOSS WILD-TYPE 41 32  5  5
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              30                41
  N1              32                32
  N2               7                 5
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   59  6
  4Q LOSS WILD-TYPE 67  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     59    6
  4Q LOSS WILD-TYPE   67    3
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              59                67
  1               6                 3
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9 76
  4Q LOSS WILD-TYPE 15 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9   76
  4Q LOSS WILD-TYPE   15   73
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               9                15
  MALE                76                73
[1] 2 2
[1] FALSE
D49V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED      23                         0    49
  4Q LOSS WILD-TYPE    18                         2    62
D49V9, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                  23                18
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  49                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    2 39
  4Q LOSS WILD-TYPE  1 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   39
  4Q LOSS WILD-TYPE    1   42
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              39                42
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED   27 18
  5P LOSS WILD-TYPE 73 53
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               45               126 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               18                53 
$`5P LOSS MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3QL 
       58.55         7.63        13.94         8.94         4.21        20.09 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB 
        3.88         0.53        17.03         4.67       122.10        60.39 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OS 
       30.25        24.00         3.68         4.70        21.01        58.59 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NR 
        2.60         3.95         3.02         2.66         5.49         8.71 
TCGA-L5-A8NT TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A4A8 TCGA-LN-A7HV 
       27.12         5.92        10.45         0.10        15.52        10.52 
TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 
       12.03        33.11        29.59         6.35         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        1.45        12.69        20.02         9.27         4.44        22.82 
TCGA-VR-A8ER TCGA-VR-AA4D TCGA-X8-AAAR 
       12.43        46.19        10.16 

$`5P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        31.27        14.30         5.92        16.24        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
       20.12        18.64         9.30         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        4.31         8.94        32.61        19.99        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         7.43         6.94         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40        55.50        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55        13.22         7.76        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09        10.36        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.10        13.15        15.35        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.00        12.23        13.18         0.13         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        8.02         7.59         5.06        14.70         7.04        53.95 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       15.78         7.00        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       15.35        18.81        19.96         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        30.71        18.18        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91         3.42         2.10         2.66        19.73 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              0.1               0.1 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           122.10             83.24 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            10.16             12.87 
[1] "0.1 - 122.1 (10.2)" "0.1 - 83.2 (12.9)" 
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         7        0        1        0         6         6
  5P LOSS WILD-TYPE       1        5        6        1        33        23
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           9          2          3          0        0
  5P LOSS WILD-TYPE        16         10          7          7        5
                   vv
clus                STAGE IVA
  5P LOSS MUTATED           1
  5P LOSS WILD-TYPE         3
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  7                 1
  STAGE IA                 0                 5
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA                6                33
  STAGE IIB                6                23
  STAGE III                9                16
  STAGE IIIA               2                10
  STAGE IIIB               3                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  5P LOSS MUTATED      13  4 19  1
  5P LOSS WILD-TYPE    18 32 66  4
D50V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              13                18
  T2                  4                32
  T3                 19                66
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5P LOSS MUTATED   16 18  3  0
  5P LOSS WILD-TYPE 55 46  9  8
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              16                55
  N1              18                46
  N2               3                 9
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED   31  1
  5P LOSS WILD-TYPE 95  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     31    1
  5P LOSS WILD-TYPE   95    8
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              31                95
  1               1                 8
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5  40
  5P LOSS WILD-TYPE  19 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5   40
  5P LOSS WILD-TYPE   19  109
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                19
  MALE                40               109
[1] 2 2
[1] FALSE
D50V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       8                         0    29
  5P LOSS WILD-TYPE    33                         2    82
D50V9, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   8                33
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  29                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2 19
  5P LOSS WILD-TYPE  1 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   19
  5P LOSS WILD-TYPE    1   62
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              19                62
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   47 32
  5Q LOSS WILD-TYPE 53 39
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               79                92 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               32                39 
$`5Q LOSS MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       32.45        20.09         2.63        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
        0.53         4.67        14.50       122.10        60.39        42.77 
TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ 
       31.56        30.25        24.00         3.68         4.70        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
       47.93         7.17         3.16        58.59         4.90         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         0.36         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       35.97        12.92        13.55         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49U 
       27.12        52.57         5.92        10.45        12.43        15.35 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HV 
       12.49        22.39        15.52        12.33        12.33        10.52 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6XG TCGA-R6-A6XQ 
       12.03        13.18        33.11         5.16        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW 
        9.30         2.89         1.45        12.69        20.02        20.38 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JE 
        8.12        28.11        42.87        46.19        10.16         2.10 
TCGA-Z6-AAPN 
        2.66 

$`5Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IC-A6RE TCGA-IC-A6RF 
       25.78        31.27        14.30         5.92         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       33.27         0.85        20.78         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA 
       23.41        12.82         9.96        14.86        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        21.70        23.18 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
       25.22        24.03         6.28         3.16         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        8.94        32.61        19.99        18.35         3.32         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.48        16.47        13.22         7.76        21.37        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       46.09        10.36        12.66        13.41         0.10        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
        0.10        13.25         0.10        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59         0.10        11.54        13.22         4.47        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.00        12.23         0.13         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO 
        5.06        14.70         7.04        53.95        15.78         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-A8EU 
        5.29         3.42         4.80        15.35         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       30.71        18.18        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-ZR-A9CJ 
        3.42        19.73 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.36              0.10 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           122.10             83.24 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            12.49             12.59 
[1] "0.4 - 122.1 (12.5)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         7        3        2        0        14        13
  5Q LOSS WILD-TYPE       1        2        5        1        25        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED          11          6          7          1        2
  5Q LOSS WILD-TYPE        14          6          3          6        3
                   vv
clus                STAGE IVA
  5Q LOSS MUTATED           3
  5Q LOSS WILD-TYPE         1
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  7                 1
  STAGE IA                 3                 2
  STAGE IB                 2                 5
  STAGE II                 0                 1
  STAGE IIA               14                25
  STAGE IIB               13                16
  STAGE III               11                14
  STAGE IIIA               6                 6
  STAGE IIIB               7                 3
  STAGE IIIC               1                 6
  STAGE IV                 2                 3
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  5Q LOSS MUTATED      18 15 38  1
  5Q LOSS WILD-TYPE    13 21 47  4
D51V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              18                13
  T2                 15                21
  T3                 38                47
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5Q LOSS MUTATED   31 33  6  1
  5Q LOSS WILD-TYPE 40 31  6  7
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              31                40
  N1              33                31
  N2               6                 6
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   57  5
  5Q LOSS WILD-TYPE 69  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     57    5
  5Q LOSS WILD-TYPE   69    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              57                69
  1               5                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   10 70
  5Q LOSS WILD-TYPE 14 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     10   70
  5Q LOSS WILD-TYPE   14   79
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              10                14
  MALE                70                79
[1] 2 2
[1] FALSE
D51V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED      17                         0    51
  5Q LOSS WILD-TYPE    24                         2    60
D51V9, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                  17                24
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  51                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2 33
  5Q LOSS WILD-TYPE  1 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2   33
  5Q LOSS WILD-TYPE    1   48
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              33                48
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   24 12
  6P LOSS WILD-TYPE 76 59
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               36               135 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12                59 
$`6P LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A5S3 TCGA-JY-A6FB TCGA-JY-A93C 
       33.27        20.09         0.53        23.41        60.39        23.18 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A88Y 
        3.16         4.31         8.94         4.70         3.16         0.36 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49N 
       16.47        13.55        83.24        52.57         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A5U7 TCGA-LN-A7HZ 
       13.41        13.25        12.59        12.49        25.25        13.18 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EQ 
        1.45        12.69        20.02         3.42         9.27        22.82 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       12.43         8.12        18.18         3.42         2.66        19.73 

$`6P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
        6.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.00         3.68        32.61        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        12.92        13.48        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37         8.71        13.41        27.12        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45        12.66         0.10        13.15        15.35         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10        12.46        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.00        12.23        12.03         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        2.89         7.00        20.38         5.29         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
        4.44        18.81        19.96         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        42.87        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE 
       15.91        10.16         2.10 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.36              0.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            83.24            122.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            12.64             12.46 
[1] "0.4 - 83.2 (12.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.3"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         2        1        0        0        11         5
  6P LOSS WILD-TYPE       6        4        7        1        28        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           4          2          2          2        0
  6P LOSS WILD-TYPE        21         10          8          5        5
                   vv
clus                STAGE IVA
  6P LOSS MUTATED           0
  6P LOSS WILD-TYPE         4
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 1                 4
  STAGE IB                 0                 7
  STAGE II                 0                 1
  STAGE IIA               11                28
  STAGE IIB                5                24
  STAGE III                4                21
  STAGE IIIA               2                10
  STAGE IIIB               2                 8
  STAGE IIIC               2                 5
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  6P LOSS MUTATED       4  4 22  1
  6P LOSS WILD-TYPE    27 32 63  4
D52V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               4                27
  T2                  4                32
  T3                 22                63
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6P LOSS MUTATED   19  7  3  2
  6P LOSS WILD-TYPE 52 57  9  6
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              19                52
  N1               7                57
  N2               3                 9
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    25   0
  6P LOSS WILD-TYPE 101   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     25    0
  6P LOSS WILD-TYPE  101    9
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              25               101
  1               0                 9
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  31
  6P LOSS WILD-TYPE  19 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   31
  6P LOSS WILD-TYPE   19  118
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               5                19
  MALE                31               118
[1] 2 2
[1] FALSE
D52V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED      11                         1    22
  6P LOSS WILD-TYPE    30                         1    89
D52V9, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                  11                30
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  22                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"
D52V10, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    1 18
  6P LOSS WILD-TYPE  2 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   18
  6P LOSS WILD-TYPE    2   63
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              18                63
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   22 15
  6Q LOSS WILD-TYPE 78 56
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               37               134 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               15                56 
$`6Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-JY-A93E 
       25.78        33.27        20.09         4.67        42.77        25.22 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.16         8.94         3.16         0.36        16.47        13.55 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49W 
       13.41        83.24        52.57         5.92        13.41        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-R6-A6XG 
       12.59        12.49        22.39        13.22        25.25        29.59 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW 
        1.45        12.69        20.02        20.38         3.42         9.27 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-Z6-A8JD 
       22.82        12.43         8.12        28.11        18.18         3.42 
TCGA-ZR-A9CJ 
       19.73 

$`6Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02         3.68        41.52        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        24.03         6.28        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        4.31        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL 
       55.50         2.66        35.97        12.92        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW 
        7.76         5.49        21.37         8.71        27.12        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S 
       10.36        10.45        12.66        12.43         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 
       15.35         0.10         0.10        12.46        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        11.54        12.33         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       33.11         5.16         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        2.89         7.00         5.29         4.80        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 
       18.81        19.96         1.55        18.31        30.71        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JE TCGA-Z6-AAPN 
        2.10         2.66 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.36              0.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            83.24            122.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           13.410            12.195 
[1] "0.4 - 83.2 (13.4)"  "0.1 - 122.1 (12.2)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0        1        1        0        11         4
  6Q LOSS WILD-TYPE       8        4        6        1        28        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           5          2          2          2        0
  6Q LOSS WILD-TYPE        20         10          8          5        5
                   vv
clus                STAGE IVA
  6Q LOSS MUTATED           1
  6Q LOSS WILD-TYPE         3
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 1                 4
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA               11                28
  STAGE IIB                4                25
  STAGE III                5                20
  STAGE IIIA               2                10
  STAGE IIIB               2                 8
  STAGE IIIC               2                 5
  STAGE IV                 0                 5
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  6Q LOSS MUTATED       3  6 21  1
  6Q LOSS WILD-TYPE    28 30 64  4
D53V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               3                28
  T2                  6                30
  T3                 21                64
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6Q LOSS MUTATED   17  9  3  2
  6Q LOSS WILD-TYPE 54 55  9  6
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              17                54
  N1               9                55
  N2               3                 9
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    24   1
  6Q LOSS WILD-TYPE 102   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     24    1
  6Q LOSS WILD-TYPE  102    8
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              24               102
  1               1                 8
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3  34
  6Q LOSS WILD-TYPE  21 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   34
  6Q LOSS WILD-TYPE   21  115
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               3                21
  MALE                34               115
[1] 2 2
[1] FALSE
D53V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED      10                         1    22
  6Q LOSS WILD-TYPE    31                         1    89
D53V9, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                  10                31
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  22                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"
D53V10, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    1 18
  6Q LOSS WILD-TYPE  2 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   18
  6Q LOSS WILD-TYPE    2   63
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              18                63
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    7  6
  7P LOSS WILD-TYPE 93 65
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               158 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6                65 
$`7P LOSS MUTATED`
TCGA-2H-A9GI TCGA-IG-A3Y9 TCGA-JY-A6FD TCGA-L5-A4OM TCGA-L5-A4OU TCGA-L5-A8NE 
       14.30         0.85        68.02        47.93        29.00        55.50 
TCGA-L5-A8NI TCGA-L5-A8NS TCGA-LN-A49L TCGA-LN-A4A8 TCGA-LN-A7HY TCGA-Q9-A6FU 
       13.48        13.41        10.45        15.52        12.03         5.16 
TCGA-VR-A8EO 
       18.81 

$`7P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        60.39         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
        6.28         3.16        30.25         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36         5.92        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        10.52        12.00        12.23        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        2.89         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.85              0.10 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            68.02            122.10 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           14.300            12.445 
[1] "0.8 - 68.0 (14.3)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.3"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        1        0        0         4         2
  7P LOSS WILD-TYPE       8        4        7        1        35        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           3          1          2          0        0
  7P LOSS WILD-TYPE        22         11          8          7        5
                   vv
clus                STAGE IVA
  7P LOSS MUTATED           0
  7P LOSS WILD-TYPE         4
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 1                 4
  STAGE IB                 0                 7
  STAGE II                 0                 1
  STAGE IIA                4                35
  STAGE IIB                2                27
  STAGE III                3                22
  STAGE IIIA               1                11
  STAGE IIIB               2                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  7P LOSS MUTATED       1  3  8  1
  7P LOSS WILD-TYPE    30 33 77  4
D54V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               1                30
  T2                  3                33
  T3                  8                77
  T4                  1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7P LOSS MUTATED    8  4  1  0
  7P LOSS WILD-TYPE 63 60 11  8
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               8                63
  N1               4                60
  N2               1                11
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    12   0
  7P LOSS WILD-TYPE 114   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     12    0
  7P LOSS WILD-TYPE  114    9
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              12               114
  1               0                 9
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3  10
  7P LOSS WILD-TYPE  21 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3   10
  7P LOSS WILD-TYPE   21  139
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3                21
  MALE                10               139
[1] 2 2
[1] FALSE
D54V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       4                         0     8
  7P LOSS WILD-TYPE    37                         2   103
D54V9, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   4                37
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   8               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    0  5
  7P LOSS WILD-TYPE  3 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    5
  7P LOSS WILD-TYPE    3   76
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5                76
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED   12 10
  7Q LOSS WILD-TYPE 88 61
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               22               149 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10                61 
$`7Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-JY-A6FD 
       25.78        14.30         5.92         0.85         0.79        68.02 
TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NS 
       29.00        55.50        13.48        13.55         8.71        13.41 
TCGA-LN-A49L TCGA-LN-A49X TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-V5-AASX 
       10.45         0.10        12.03        33.11         5.06         4.44 
TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-AA7I TCGA-Z6-AAPN 
       18.81         1.55        15.91         2.66 

$`7Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        4.67        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.95         3.02         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT 
       16.47        13.22         7.76         5.49        21.37        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       83.24        52.57        46.09        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18         0.13         5.16         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        9.17        10.16         3.42         2.10        19.73 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              0.1               0.1 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            68.02            122.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            12.72             12.59 
[1] "0.1 - 68.0 (12.7)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         0        0        1        0         8         2
  7Q LOSS WILD-TYPE       8        5        6        1        31        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           7          1          1          0        0
  7Q LOSS WILD-TYPE        18         11          9          7        5
                   vv
clus                STAGE IVA
  7Q LOSS MUTATED           0
  7Q LOSS WILD-TYPE         4
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 5
  STAGE IB                 1                 6
  STAGE II                 0                 1
  STAGE IIA                8                31
  STAGE IIB                2                27
  STAGE III                7                18
  STAGE IIIA               1                11
  STAGE IIIB               1                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  7Q LOSS MUTATED       0  3 15  2
  7Q LOSS WILD-TYPE    31 33 70  3
D55V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               0                31
  T2                  3                33
  T3                 15                70
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7Q LOSS MUTATED   13  7  0  0
  7Q LOSS WILD-TYPE 58 57 12  8
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              13                58
  N1               7                57
  N2               0                12
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    20   0
  7Q LOSS WILD-TYPE 106   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     20    0
  7Q LOSS WILD-TYPE  106    9
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              20               106
  1               0                 9
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3  19
  7Q LOSS WILD-TYPE  21 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3   19
  7Q LOSS WILD-TYPE   21  130
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                21
  MALE                19               130
[1] 2 2
[1] FALSE
D55V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       4                         0    13
  7Q LOSS WILD-TYPE    37                         2    98
D55V9, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   4                37
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  13                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    0  8
  7Q LOSS WILD-TYPE  3 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    8
  7Q LOSS WILD-TYPE    3   73
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               8                73
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   36 21
  8P LOSS WILD-TYPE 64 50
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               57               114 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               21                50 
$`8P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
       25.78         5.92        13.94         7.69         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12         3.88         0.53         0.79        23.41         9.96 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E 
       14.50        44.75        60.39        25.41        23.18        25.22 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
        8.94        24.00         3.68        32.61        21.01         3.32 
TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NN 
        7.43         7.40         3.95        55.50         2.66         5.49 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A1 
        8.71        27.12        12.66        12.43        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW 
       12.49        22.39        12.33        13.22        12.33        12.00 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB 
        5.16         7.82         8.02         1.45        20.38         5.29 
TCGA-V5-A7RC TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G 
        3.42        12.43        18.31        28.11        42.87        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-AAPN 
        9.17        15.91         2.66 

$`8P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        14.30        58.55         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         6.21        33.27        20.09        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       18.64         9.30        17.03        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        68.02         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30         4.31         4.70        19.99        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         7.76        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R 
       46.09        10.36         5.92        10.45        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 
       13.15        15.35         0.10        13.25         0.10        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59         0.10        15.52        11.54         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.23        12.03        13.18         0.13        33.11 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.02         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       19.96        22.82         1.55         8.12        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       46.19        11.24        10.16         3.42         2.10        19.73 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.53              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            60.39            122.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            12.43             12.87 
[1] "0.5 - 60.4 (12.4)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "1"  
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         3        0        2        0        10        13
  8P LOSS WILD-TYPE       5        5        5        1        29        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           7          7          5          2        1
  8P LOSS WILD-TYPE        18          5          5          5        4
                   vv
clus                STAGE IVA
  8P LOSS MUTATED           2
  8P LOSS WILD-TYPE         2
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 0                 5
  STAGE IB                 2                 5
  STAGE II                 0                 1
  STAGE IIA               10                29
  STAGE IIB               13                16
  STAGE III                7                18
  STAGE IIIA               7                 5
  STAGE IIIB               5                 5
  STAGE IIIC               2                 5
  STAGE IV                 1                 4
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8P LOSS MUTATED      11 13 28  3
  8P LOSS WILD-TYPE    20 23 57  2
D56V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              11                20
  T2                 13                23
  T3                 28                57
  T4                  3                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8P LOSS MUTATED   19 26  7  2
  8P LOSS WILD-TYPE 52 38  5  6
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              19                52
  N1              26                38
  N2               7                 5
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   47  3
  8P LOSS WILD-TYPE 79  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     47    3
  8P LOSS WILD-TYPE   79    6
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              47                79
  1               3                 6
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    7 51
  8P LOSS WILD-TYPE 17 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7   51
  8P LOSS WILD-TYPE   17   98
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               7                17
  MALE                51                98
[1] 2 2
[1] FALSE
D56V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED      15                         1    33
  8P LOSS WILD-TYPE    26                         1    78
D56V9, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                  15                26
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  33                78
[1] 3 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, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1 28
  8P LOSS WILD-TYPE  2 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   28
  8P LOSS WILD-TYPE    2   53
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              28                53
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED   16  6
  8Q LOSS WILD-TYPE 84 65
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               149 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                6                65 
$`8Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-IG-A5S3 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A93E 
       25.78         5.92        23.41        44.75        60.39        25.22 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A891 TCGA-L5-A8NE 
        8.94         3.68        32.61        21.01         3.95        55.50 
TCGA-L5-A8NF TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW 
        2.66        12.43        12.46        13.22        12.33        12.00 
TCGA-V5-A7RC TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-Z6-AAPN 
        3.42        28.11        42.87         2.66 

$`8Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       16.24         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        3.88         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM 
        0.30         4.31        24.00         4.70        19.99        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NG 
        2.60        25.12         0.36         7.40         3.02        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        5.49        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 
        0.10        15.52        11.54        12.33         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        2.89         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10        19.73 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             2.66              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            60.39            122.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            12.84             12.59 
[1] "2.7 - 60.4 (12.8)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "2"  
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         3        0        0        0         4         6
  8Q LOSS WILD-TYPE       5        5        7        1        35        23
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           2          2          0          0        0
  8Q LOSS WILD-TYPE        23         10         10          7        5
                   vv
clus                STAGE IVA
  8Q LOSS MUTATED           2
  8Q LOSS WILD-TYPE         2
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 0                 5
  STAGE IB                 0                 7
  STAGE II                 0                 1
  STAGE IIA                4                35
  STAGE IIB                6                23
  STAGE III                2                23
  STAGE IIIA               2                10
  STAGE IIIB               0                10
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8Q LOSS MUTATED       6  6  9  0
  8Q LOSS WILD-TYPE    25 30 76  5
D57V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               6                25
  T2                  6                30
  T3                  9                76
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q LOSS MUTATED    9 11  1  0
  8Q LOSS WILD-TYPE 62 53 11  8
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               9                62
  N1              11                53
  N2               1                11
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    17   2
  8Q LOSS WILD-TYPE 109   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     17    2
  8Q LOSS WILD-TYPE  109    7
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              17               109
  1               2                 7
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     3  19
  8Q LOSS WILD-TYPE  21 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3   19
  8Q LOSS WILD-TYPE   21  130
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                21
  MALE                19               130
[1] 2 2
[1] FALSE
D57V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       6                         1    11
  8Q LOSS WILD-TYPE    35                         1   100
D57V9, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   6                35
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  11               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    0  8
  8Q LOSS WILD-TYPE  3 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    8
  8Q LOSS WILD-TYPE    3   73
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               8                73
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   60 35
  9P LOSS WILD-TYPE 40 36
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               95                76 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               35                36 
$`9P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        7.69        20.78        20.12        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
        0.79        23.41         9.96         4.67        14.50        12.16 
TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF 
       60.39        25.41        25.22         3.16         8.94         3.68 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
       32.61        47.93        18.35         3.32         7.17        58.59 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE 
        7.13         7.43         6.94         2.60         3.95        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS 
        2.66        35.97        16.47        13.22         8.71        13.41 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S 
       83.24        10.36        10.45        12.66        12.43        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25         0.10        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.76        22.39         0.10        15.52        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        0.13        33.11         5.16         5.06        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
        6.35         9.30        15.78         1.45        12.69        20.02 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42         4.80         9.27         4.44        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       42.87        46.19        10.16         3.42        19.73 

$`9P LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IC-A6RF 
       58.55         7.63         5.92        13.94        32.45         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
       33.27        20.09         0.85         2.63         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       12.82        14.86       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       41.52        42.77        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
        6.28        30.25         0.30         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       19.99        21.01         1.38         3.16         4.90        29.00 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH 
        8.71        25.12         0.36         7.40         3.02        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT 
       13.48        13.55         7.76         5.49        21.37        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V 
       52.57        46.09         5.92        13.41         0.10         0.10 
TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HZ TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.59        11.54         4.47        13.18         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW 
        7.59         7.04        53.95         2.89         7.00        20.38 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
       15.35        19.96        30.71        18.18        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91         2.10         2.66 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              0.1               0.1 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.24            122.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            12.43             13.05 
[1] "0.1 - 83.2 (12.4)"  "0.1 - 122.1 (13.1)"
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         2        2        4        1        21        17
  9P LOSS WILD-TYPE       6        3        3        0        18        12
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED          15          6          5          3        1
  9P LOSS WILD-TYPE        10          6          5          4        4
                   vv
clus                STAGE IVA
  9P LOSS MUTATED           4
  9P LOSS WILD-TYPE         0
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 4                 3
  STAGE II                 1                 0
  STAGE IIA               21                18
  STAGE IIB               17                12
  STAGE III               15                10
  STAGE IIIA               6                 6
  STAGE IIIB               5                 5
  STAGE IIIC               3                 4
  STAGE IV                 1                 4
  STAGE IVA                4                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  9P LOSS MUTATED      15 23 45  2
  9P LOSS WILD-TYPE    16 13 40  3
D58V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              15                16
  T2                 23                13
  T3                 45                40
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9P LOSS MUTATED   35 41  5  3
  9P LOSS WILD-TYPE 36 23  7  5
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              35                36
  N1              41                23
  N2               5                 7
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   68  5
  9P LOSS WILD-TYPE 58  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     68    5
  9P LOSS WILD-TYPE   58    4
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              68                58
  1               5                 4
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    8 88
  9P LOSS WILD-TYPE 16 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8   88
  9P LOSS WILD-TYPE   16   61
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               8                16
  MALE                88                61
[1] 2 2
[1] FALSE
D58V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED      28                         1    54
  9P LOSS WILD-TYPE    13                         1    57
D58V9, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                  28                13
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  54                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    3 51
  9P LOSS WILD-TYPE  0 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3   51
  9P LOSS WILD-TYPE    0   30
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 0
  NOT HISPANIC OR LATINO              51                30
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   36 25
  9Q LOSS WILD-TYPE 64 46
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               61               110 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               25                46 
$`9Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
       25.78        31.27        16.24         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
       18.64         3.88         0.79        23.41         9.96         4.67 
TCGA-IG-A97H TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS 
       14.50        25.22         8.94         3.68        47.93        58.59 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.13         6.94         2.60        55.50         2.66        35.97 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       13.22        13.41        83.24        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 
       12.43        13.15        12.46        12.59        12.76         0.10 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO 
       12.33        10.52        12.00        12.23        12.03         0.13 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
        5.06        29.59         6.35         9.30        15.78        12.69 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EW 
        5.29         3.42         4.80        18.81         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       28.11        42.87        11.24        10.16         3.42         2.10 
TCGA-ZR-A9CJ 
       19.73 

$`9Q LOSS WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP 
        2.63         9.30         0.53        17.03        12.82        14.86 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       24.00         4.70        32.61        19.99        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        7.43         8.71        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        3.02        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        27.12        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        5.92        13.41         0.10        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.10        12.49        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-M9-A5M8 
       12.33        13.22         4.47        25.25        13.18        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       53.95         2.89         1.45         7.00        20.02        20.38 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         4.44        19.96        22.82        12.43 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       18.31        30.71        18.18        46.19        15.06         9.17 
TCGA-VR-AA7I TCGA-Z6-AAPN 
       15.91         2.66 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              0.1               0.1 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            83.24            122.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            12.23             13.20 
[1] "0.1 - 83.2 (12.2)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         0        1        3        1        12        12
  9Q LOSS WILD-TYPE       8        4        4        0        27        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           6          6          4          2        1
  9Q LOSS WILD-TYPE        19          6          6          5        4
                   vv
clus                STAGE IVA
  9Q LOSS MUTATED           4
  9Q LOSS WILD-TYPE         0
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 1                 4
  STAGE IB                 3                 4
  STAGE II                 1                 0
  STAGE IIA               12                27
  STAGE IIB               12                17
  STAGE III                6                19
  STAGE IIIA               6                 6
  STAGE IIIB               4                 6
  STAGE IIIC               2                 5
  STAGE IV                 1                 4
  STAGE IVA                4                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  9Q LOSS MUTATED       8 16 29  2
  9Q LOSS WILD-TYPE    23 20 56  3
D59V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1               8                23
  T2                 16                20
  T3                 29                56
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9Q LOSS MUTATED   23 24  4  3
  9Q LOSS WILD-TYPE 48 40  8  5
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              23                48
  N1              24                40
  N2               4                 8
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   41  5
  9Q LOSS WILD-TYPE 85  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     41    5
  9Q LOSS WILD-TYPE   85    4
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              41                85
  1               5                 4
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    6 55
  9Q LOSS WILD-TYPE 18 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6   55
  9Q LOSS WILD-TYPE   18   94
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               6                18
  MALE                55                94
[1] 2 2
[1] FALSE
D59V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED      17                         1    36
  9Q LOSS WILD-TYPE    24                         1    75
D59V9, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                  17                24
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  36                75
[1] 3 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, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    3 35
  9Q LOSS WILD-TYPE  0 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3   35
  9Q LOSS WILD-TYPE    0   46
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 0
  NOT HISPANIC OR LATINO              35                46
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   26 17
  10P LOSS WILD-TYPE 74 54
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                43                128 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                 54 
$`10P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A50L 
       25.78        14.30         5.92        33.27         0.85         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43J 
        0.79        23.41        14.50        23.18         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW 
        8.94        24.00         4.70         3.32         4.90         7.13 
TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O 
       13.55        13.41        27.12        83.24        12.66        13.41 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        12.33        13.22         4.47        25.25        12.00 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP 
       13.18         0.13         7.82         3.42         4.80        19.96 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-Z6-A8JD 
        8.12        28.11        18.18        15.06        11.24         3.42 
TCGA-Z6-AAPN 
        2.66 

$`10P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69         6.21        20.09        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.16        30.25         3.68        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        5.49        21.37         8.71        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        5.92        10.45        12.43         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
        0.10        13.25         0.10        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U6 
       12.76        12.59        22.39         0.10        15.52        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN 
       10.52        12.23        12.03        33.11         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.02        20.38         5.29        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        22.82        12.43         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       30.71        42.87        46.19         9.17        15.91        10.16 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.13               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             83.24             122.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             12.00              12.64 
[1] "0.1 - 83.2 (12.0)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         1        0        2        0        13         7
  10P LOSS WILD-TYPE       7        5        5        1        26        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           5          3          5          2        3
  10P LOSS WILD-TYPE        20          9          5          5        2
                    vv
clus                 STAGE IVA
  10P LOSS MUTATED           1
  10P LOSS WILD-TYPE         3
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  2                  5
  STAGE II                  0                  1
  STAGE IIA                13                 26
  STAGE IIB                 7                 22
  STAGE III                 5                 20
  STAGE IIIA                3                  9
  STAGE IIIB                5                  5
  STAGE IIIC                2                  5
  STAGE IV                  3                  2
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  10P LOSS MUTATED       3 11 28  1
  10P LOSS WILD-TYPE    28 25 57  4
D60V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1                3                 28
  T2                  11                 25
  T3                  28                 57
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10P LOSS MUTATED   21 11  7  3
  10P LOSS WILD-TYPE 50 53  5  5
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               21                 50
  N1               11                 53
  N2                7                  5
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   36  4
  10P LOSS WILD-TYPE 90  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     36    4
  10P LOSS WILD-TYPE   90    5
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               36                 90
  1                4                  5
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     8  36
  10P LOSS WILD-TYPE  16 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8   36
  10P LOSS WILD-TYPE   16  113
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                8                 16
  MALE                 36                113
[1] 2 2
[1] FALSE
D60V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED      15                         1    22
  10P LOSS WILD-TYPE    26                         1    89
D60V9, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                   15                 26
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   22                 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"
D60V10, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    0 22
  10P LOSS WILD-TYPE  3 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0   22
  10P LOSS WILD-TYPE    3   59
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               22                 59
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   27 15
  10Q LOSS WILD-TYPE 73 56
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                42                129 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                 56 
$`10Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB 
       25.78        14.30         5.92        33.27         0.85         2.63 
TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H 
        0.53        23.41        14.50        23.18         3.16         0.30 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NK 
       24.00         4.70         3.32         4.90         7.13        13.55 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 
       27.12        83.24        12.66         0.10        12.46        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       22.39         0.10        11.54        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-V5-A7RC 
       25.25        12.00        12.03        13.18         5.16         3.42 
TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-Z6-A8JE TCGA-Z6-AAPN 
        4.80        19.96        28.11        18.18         2.10         2.66 

$`10Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69         6.21        20.09        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
       30.25         4.31         8.94         3.68        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       58.59        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35         0.10        13.25         0.10        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       12.76        12.59        15.52         4.47        10.52        12.23 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.38         5.29        15.35         9.27         4.44        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       10.16         3.42        19.73 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               0.1                0.1 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             83.24             122.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             12.33              12.76 
[1] "0.1 - 83.2 (12.3)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         1        0        1        1        14         5
  10Q LOSS WILD-TYPE       7        5        6        0        25        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           7          4          4          2        1
  10Q LOSS WILD-TYPE        18          8          6          5        4
                    vv
clus                 STAGE IVA
  10Q LOSS MUTATED           1
  10Q LOSS WILD-TYPE         3
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  1                  6
  STAGE II                  1                  0
  STAGE IIA                14                 25
  STAGE IIB                 5                 24
  STAGE III                 7                 18
  STAGE IIIA                4                  8
  STAGE IIIB                4                  6
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  10Q LOSS MUTATED       3 12 25  1
  10Q LOSS WILD-TYPE    28 24 60  4
D61V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                3                 28
  T2                  12                 24
  T3                  25                 60
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10Q LOSS MUTATED   19 15  4  2
  10Q LOSS WILD-TYPE 52 49  8  6
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               19                 52
  N1               15                 49
  N2                4                  8
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   38  2
  10Q LOSS WILD-TYPE 88  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     38    2
  10Q LOSS WILD-TYPE   88    7
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               38                 88
  1                2                  7
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6  37
  10Q LOSS WILD-TYPE  18 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   37
  10Q LOSS WILD-TYPE   18  112
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                6                 18
  MALE                 37                112
[1] 2 2
[1] FALSE
D61V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED      18                         1    19
  10Q LOSS WILD-TYPE    23                         1    92
D61V9, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                   18                 23
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   19                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    0 26
  10Q LOSS WILD-TYPE  3 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0   26
  10Q LOSS WILD-TYPE    3   55
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               26                 55
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   33 14
  11P LOSS WILD-TYPE 67 57
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                47                124 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                14                 57 
$`11P LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YB 
       31.27        14.30         5.92         4.21         0.85         2.63 
TCGA-JY-A938 TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OP 
       25.41         3.16         0.30         4.70         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE 
        3.16         6.94         2.60         0.36         3.02        55.50 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       16.47        13.55        13.22        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.43        13.41         0.10        13.25        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6KZ 
       12.76         0.10        12.33        12.03         0.13         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE 
       29.59         6.35         2.89         1.45        12.69         4.80 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EX TCGA-Z6-A8JE 
        9.27        18.81        12.43        28.11         2.10 

$`11P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
       32.45         7.69         6.21        33.27        20.09        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.50        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        42.77        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M 
       25.22        24.03         6.28        30.25         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.00         3.68        32.61        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         1.38        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF 
        7.43         8.71        25.12         7.40         3.95         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       35.97        12.92        13.48         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
        5.92        13.15        15.35         0.10         0.10        12.46 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        25.25        10.52        12.00        12.23        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       33.11         5.16         7.82         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04        53.95         9.30        15.78         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP 
       20.38         5.29         3.42        15.35         4.44        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       22.82         1.55        18.31         8.12        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       10.16         3.42         2.66        19.73 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               0.1                0.1 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              55.5              122.1 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              9.27              13.71 
[1] "0.1 - 55.5 (9.3)"   "0.1 - 122.1 (13.7)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         2        2        2        1         7         5
  11P LOSS WILD-TYPE       6        3        5        0        32        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED          12          3          1          2        0
  11P LOSS WILD-TYPE        13          9          9          5        5
                    vv
clus                 STAGE IVA
  11P LOSS MUTATED           1
  11P LOSS WILD-TYPE         3
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  2                  3
  STAGE IB                  2                  5
  STAGE II                  1                  0
  STAGE IIA                 7                 32
  STAGE IIB                 5                 24
  STAGE III                12                 13
  STAGE IIIA                3                  9
  STAGE IIIB                1                  9
  STAGE IIIC                2                  5
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  11P LOSS MUTATED       8  7 22  2
  11P LOSS WILD-TYPE    23 29 63  3
D62V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1                8                 23
  T2                   7                 29
  T3                  22                 63
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11P LOSS MUTATED   18 19  0  2
  11P LOSS WILD-TYPE 53 45 12  6
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               18                 53
  N1               19                 45
  N2                0                 12
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   32  1
  11P LOSS WILD-TYPE 94  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     32    1
  11P LOSS WILD-TYPE   94    8
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               32                 94
  1                1                  8
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4  43
  11P LOSS WILD-TYPE  20 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4   43
  11P LOSS WILD-TYPE   20  106
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                4                 20
  MALE                 43                106
[1] 2 2
[1] FALSE
D62V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED      13                         0    28
  11P LOSS WILD-TYPE    28                         2    83
D62V9, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                   13                 28
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   28                 83
[1] 3 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, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    1 23
  11P LOSS WILD-TYPE  2 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1   23
  11P LOSS WILD-TYPE    2   58
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               23                 58
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   32 20
  11Q LOSS WILD-TYPE 68 51
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                52                119 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                20                 51 
$`11Q LOSS MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A6QS 
        5.92         4.21        20.12        18.64        23.41         9.96 
TCGA-IG-A97I TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OG TCGA-L5-A4OM TCGA-L5-A4OO 
       12.16         3.16         0.30         4.70        47.93         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE 
        7.17         3.16         6.94         2.60         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L 
        2.66        13.55        13.22        27.12        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.66         0.10         0.10        13.25        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY 
       12.76         0.10        15.52        12.33        25.25        12.03 
TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        0.13         5.06         6.35         2.89         1.45        12.69 
TCGA-S8-A6BV TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EX 
       20.02         3.42        18.81        12.43        18.31        28.11 
TCGA-VR-A8EZ TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
       18.18         9.17        15.91         2.10 

$`11Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94        16.24        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09         0.85        20.78         2.63         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03         0.79        12.82        14.86         4.67 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M 
       25.22        24.03         6.28        30.25         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
       24.00         3.68        32.61        19.99        21.01        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG 
        8.71        25.12         0.36         7.40         3.95        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.48        16.47         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
        8.71        13.41        83.24        52.57        46.09         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       12.43        13.41        13.15        15.35         0.10        12.46 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        22.39        11.54        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
       10.52        12.00        12.23        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        14.70         7.04        29.59 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30        15.78         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        19.96        22.82 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        1.55         8.12        30.71        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24        10.16         3.42         2.66        19.73 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               0.1                0.1 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              55.5              122.1 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             11.24              13.22 
[1] "0.1 - 55.5 (11.2)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.4"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         2        3        1        1        10         6
  11Q LOSS WILD-TYPE       6        2        6        0        29        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED          11          3          1          4        1
  11Q LOSS WILD-TYPE        14          9          9          3        4
                    vv
clus                 STAGE IVA
  11Q LOSS MUTATED           2
  11Q LOSS WILD-TYPE         2
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  3                  2
  STAGE IB                  1                  6
  STAGE II                  1                  0
  STAGE IIA                10                 29
  STAGE IIB                 6                 23
  STAGE III                11                 14
  STAGE IIIA                3                  9
  STAGE IIIB                1                  9
  STAGE IIIC                4                  3
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  11Q LOSS MUTATED       8 11 24  2
  11Q LOSS WILD-TYPE    23 25 61  3
D63V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1                8                 23
  T2                  11                 25
  T3                  24                 61
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11Q LOSS MUTATED   22 19  0  4
  11Q LOSS WILD-TYPE 49 45 12  4
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               22                 49
  N1               19                 45
  N2                0                 12
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   35  3
  11Q LOSS WILD-TYPE 91  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     35    3
  11Q LOSS WILD-TYPE   91    6
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               35                 91
  1                3                  6
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6  46
  11Q LOSS WILD-TYPE  18 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6   46
  11Q LOSS WILD-TYPE   18  103
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                6                 18
  MALE                 46                103
[1] 2 2
[1] FALSE
D63V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED      14                         1    32
  11Q LOSS WILD-TYPE    27                         1    79
D63V9, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                   14                 27
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   32                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    1 26
  11Q LOSS WILD-TYPE  2 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   26
  11Q LOSS WILD-TYPE    2   55
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               26                 55
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   19 13
  12P LOSS WILD-TYPE 81 58
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                32                139 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                13                 58 
$`12P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4QS 
       25.78        31.27        13.94        32.45        33.27         3.88 
TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E 
        0.79        14.50        42.77        25.41        25.22        30.25 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
        8.94        32.61         7.17         1.38        58.59         7.13 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NV TCGA-LN-A49M 
        3.95         3.02        55.50        12.92        52.57        12.66 
TCGA-LN-A7HY TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-S8-A6BV TCGA-V5-A7RC TCGA-X8-AAAR 
       12.03         7.82         5.06        20.02         3.42        10.16 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

$`12P LOSS WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21         7.69         6.21        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
        0.30         4.31        24.00         3.68         4.70        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT 
       21.01        47.93        18.35         3.32         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        0.36         7.40         2.66        35.97        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        83.24        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.43        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
        0.10        13.25         0.10        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.00        12.23        13.18         0.13        33.11         5.16 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        4.44        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       46.19        15.06        11.24         9.17        15.91         3.42 
TCGA-Z6-AAPN 
        2.66 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.79               0.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             58.59             122.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             13.43              12.46 
[1] "0.8 - 58.6 (13.4)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.3"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         3        1        1        0         5         7
  12P LOSS WILD-TYPE       5        4        6        1        34        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           2          4          2          1        1
  12P LOSS WILD-TYPE        23          8          8          6        4
                    vv
clus                 STAGE IVA
  12P LOSS MUTATED           0
  12P LOSS WILD-TYPE         4
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 5                 34
  STAGE IIB                 7                 22
  STAGE III                 2                 23
  STAGE IIIA                4                  8
  STAGE IIIB                2                  8
  STAGE IIIC                1                  6
  STAGE IV                  1                  4
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  12P LOSS MUTATED       8  6 16  0
  12P LOSS WILD-TYPE    23 30 69  5
D64V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                8                 23
  T2                   6                 30
  T3                  16                 69
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  12P LOSS MUTATED   11 13  4  1
  12P LOSS WILD-TYPE 60 51  8  7
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               11                 60
  N1               13                 51
  N2                4                  8
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    23   1
  12P LOSS WILD-TYPE 103   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     23    1
  12P LOSS WILD-TYPE  103    8
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               23                103
  1                1                  8
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     6  26
  12P LOSS WILD-TYPE  18 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6   26
  12P LOSS WILD-TYPE   18  123
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                6                 18
  MALE                 26                123
[1] 2 2
[1] FALSE
D64V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       3                         1    22
  12P LOSS WILD-TYPE    38                         1    89
D64V9, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    3                 38
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   22                 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"
D64V10, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    0 13
  12P LOSS WILD-TYPE  3 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   13
  12P LOSS WILD-TYPE    3   68
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               13                 68
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED   17 11
  12Q LOSS WILD-TYPE 83 60
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                28                143 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                11                 60 
$`12Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 
       31.27        13.94        33.27         3.88         0.79        23.41 
TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43M 
       14.50        42.77        25.41        25.22        30.25         8.94 
TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A893 TCGA-L5-A8NE 
       32.61         7.17        58.59         7.13         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-S8-A6BV 
        2.66        12.92         7.82         5.06         2.89        20.02 
TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-A8ET TCGA-X8-AAAR 
        3.42         4.44         1.55        10.16 

$`12Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69         6.21        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         0.30         4.31        24.00         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       19.99        21.01        47.93        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        3.16         4.90        29.00         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG 
        2.60        25.12         0.36         7.40         3.95        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN 
       12.03        13.18         0.13        33.11         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         1.45        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        5.29         4.80        15.35         9.27        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91         3.42         2.10         2.66        19.73 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.79               0.10 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             58.59             122.10 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             11.54              12.59 
[1] "0.8 - 58.6 (11.5)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         3        1        1        0         3         8
  12Q LOSS WILD-TYPE       5        4        6        1        36        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0          2          2          0        1
  12Q LOSS WILD-TYPE        25         10          8          7        4
                    vv
clus                 STAGE IVA
  12Q LOSS MUTATED           1
  12Q LOSS WILD-TYPE         3
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 3                 36
  STAGE IIB                 8                 21
  STAGE III                 0                 25
  STAGE IIIA                2                 10
  STAGE IIIB                2                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  12Q LOSS MUTATED       9  5 10  0
  12Q LOSS WILD-TYPE    22 31 75  5
D65V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1                9                 22
  T2                   5                 31
  T3                  10                 75
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  12Q LOSS MUTATED   11  9  3  0
  12Q LOSS WILD-TYPE 60 55  9  8
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               11                 60
  N1                9                 55
  N2                3                  9
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    18   2
  12Q LOSS WILD-TYPE 108   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     18    2
  12Q LOSS WILD-TYPE  108    7
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               18                108
  1                2                  7
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     7  21
  12Q LOSS WILD-TYPE  17 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      7   21
  12Q LOSS WILD-TYPE   17  128
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                7                 17
  MALE                 21                128
[1] 2 2
[1] FALSE
D65V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       1                         1    22
  12Q LOSS WILD-TYPE    40                         1    89
D65V9, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    1                 40
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   22                 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"
D65V10, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    0 12
  12Q LOSS WILD-TYPE  3 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   12
  12Q LOSS WILD-TYPE    3   69
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               12                 69
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   37 24
  13Q LOSS WILD-TYPE 63 47
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                61                110 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                24                 47 
$`13Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE 
       25.78        58.55         7.63         8.94        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
       20.09         0.85        20.78         3.88         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A93E 
       23.41         9.96        44.75        60.39        68.02        25.22 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
       24.00         3.68        21.01        47.93         3.16        29.00 
TCGA-L5-A891 TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
        3.95        13.22         5.49        13.41        83.24        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       15.35        13.25        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
        0.10        13.22        12.33        10.52        12.23        12.03 
TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-VR-A8EO 
        0.13         5.06        29.59         6.35        12.69        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 
       19.96        22.82        18.31        28.11        18.18        42.87 
TCGA-VR-AA7I 
       15.91 

$`13Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        6.21        33.27         2.63        20.12        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
        0.79        12.82        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
      122.10         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        0.30         4.31         8.94         4.70        32.61        19.99 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49V 
        8.71        27.12        52.57        46.09        12.66         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10        12.46        12.59        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
        4.47        25.25        12.00        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        7.82         8.02         7.59        14.70         7.04        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         2.89         1.45         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D 
        4.44        12.43         1.55         8.12        30.71        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.06        11.24         9.17        10.16         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               0.1                0.1 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             83.24             122.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             13.22              11.77 
[1] "0.1 - 83.2 (13.2)"  "0.1 - 122.1 (11.8)"
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         3        2        0        1        15        11
  13Q LOSS WILD-TYPE       5        3        7        0        24        18
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED          12          5          4          2        1
  13Q LOSS WILD-TYPE        13          7          6          5        4
                    vv
clus                 STAGE IVA
  13Q LOSS MUTATED           1
  13Q LOSS WILD-TYPE         3
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  2                  3
  STAGE IB                  0                  7
  STAGE II                  1                  0
  STAGE IIA                15                 24
  STAGE IIB                11                 18
  STAGE III                12                 13
  STAGE IIIA                5                  7
  STAGE IIIB                4                  6
  STAGE IIIC                2                  5
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  13Q LOSS MUTATED      10 13 32  3
  13Q LOSS WILD-TYPE    21 23 53  2
D66V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               10                 21
  T2                  13                 23
  T3                  32                 53
  T4                   3                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  13Q LOSS MUTATED   28 25  3  2
  13Q LOSS WILD-TYPE 43 39  9  6
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               28                 43
  N1               25                 39
  N2                3                  9
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   51  2
  13Q LOSS WILD-TYPE 75  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     51    2
  13Q LOSS WILD-TYPE   75    7
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               51                 75
  1                2                  7
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    4 58
  13Q LOSS WILD-TYPE 20 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   58
  13Q LOSS WILD-TYPE   20   91
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 20
  MALE                 58                 91
[1] 2 2
[1] FALSE
D66V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED      23                         0    33
  13Q LOSS WILD-TYPE    18                         2    78
D66V9, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                   23                 18
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   33                 78
[1] 3 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, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    1 32
  13Q LOSS WILD-TYPE  2 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   32
  13Q LOSS WILD-TYPE    2   49
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               32                 49
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   24 19
  14Q LOSS WILD-TYPE 76 52
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                43                128 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                 52 
$`14Q LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
        7.63         8.94        16.24         4.21        32.45        20.09 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB 
       23.41        12.82         4.67        14.50       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.22         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A891 
        4.70        32.61         7.13         6.94         0.36         3.95 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49W 
       55.50         2.66        16.47        10.36        10.45        13.25 
TCGA-LN-A7HV TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 
       10.52        33.11         7.59         5.06         6.35         9.30 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       15.78         7.00        18.81        22.82        42.87        15.06 
TCGA-Z6-AAPN 
        2.66 

$`14Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        0.79         9.96        14.86        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI 
       24.03         6.28         3.16        30.25         4.31        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T 
        3.16        58.59         4.90        29.00         7.43         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH 
        2.60        25.12         7.40         3.02        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35         0.10         0.10        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.23        12.03        13.18         0.13         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 
        8.02        14.70         7.04        29.59        53.95         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        1.45        12.69        20.02        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER 
        4.80        15.35         9.27         4.44        19.96        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       46.19        11.24         9.17        15.91        10.16         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               0.3                0.1 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            122.10              83.24 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             10.52              12.59 
[1] "0.3 - 122.1 (10.5)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         4        0        1        0         6         7
  14Q LOSS WILD-TYPE       4        5        6        1        33        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           7          3          4          1        0
  14Q LOSS WILD-TYPE        18          9          6          6        5
                    vv
clus                 STAGE IVA
  14Q LOSS MUTATED           3
  14Q LOSS WILD-TYPE         1
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  0                  5
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 6                 33
  STAGE IIB                 7                 22
  STAGE III                 7                 18
  STAGE IIIA                3                  9
  STAGE IIIB                4                  6
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  14Q LOSS MUTATED       8  6 25  0
  14Q LOSS WILD-TYPE    23 30 60  5
D67V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1                8                 23
  T2                   6                 30
  T3                  25                 60
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  14Q LOSS MUTATED   15 17  5  1
  14Q LOSS WILD-TYPE 56 47  7  7
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               15                 56
  N1               17                 47
  N2                5                  7
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   30  3
  14Q LOSS WILD-TYPE 96  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     30    3
  14Q LOSS WILD-TYPE   96    6
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               30                 96
  1                3                  6
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     7  36
  14Q LOSS WILD-TYPE  17 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      7   36
  14Q LOSS WILD-TYPE   17  113
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                7                 17
  MALE                 36                113
[1] 2 2
[1] FALSE
D67V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       6                         0    29
  14Q LOSS WILD-TYPE    35                         2    82
D67V9, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    6                 35
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   29                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    1 14
  14Q LOSS WILD-TYPE  2 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   14
  14Q LOSS WILD-TYPE    2   67
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               14                 67
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   30 20
  15Q LOSS WILD-TYPE 70 51
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                50                121 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                20                 51 
$`15Q LOSS MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YC 
        5.92        16.24        32.45         7.69        20.09        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A938 TCGA-JY-A93C 
       18.64         3.88         4.67        14.50        25.41        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       31.56        25.22         0.30         8.94        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NE 
       32.61        47.93         4.90        29.00         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NR 
        2.66        35.97        12.92        13.48         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ 
       13.41        27.12        83.24        12.59        22.39        12.33 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-RE-A7BO 
       12.33        25.25        12.03         5.06        29.59         7.00 
TCGA-S8-A6BV TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EU TCGA-X8-AAAR TCGA-Z6-A8JE 
       20.02         4.80        18.81        18.31        10.16         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`15Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94         4.21         6.21        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82         9.96        14.86        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       60.39        68.02         3.68        41.52        42.77        21.70 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         4.31         3.68 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        3.16        58.59         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ 
        2.60        25.12         0.36         7.40         3.95        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW 
       13.55        13.22         7.76        21.37        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.49        12.76        12.59         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       11.54        13.22         4.47        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         1.45        12.69        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        3.42        15.35         9.27         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD 
        3.42 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               0.3                0.1 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             83.24             122.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             13.99              12.43 
[1] "0.3 - 83.2 (14.0)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         3        1        1        0         8        10
  15Q LOSS WILD-TYPE       5        4        6        1        31        19
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           8          4          5          2        3
  15Q LOSS WILD-TYPE        17          8          5          5        2
                    vv
clus                 STAGE IVA
  15Q LOSS MUTATED           2
  15Q LOSS WILD-TYPE         2
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 8                 31
  STAGE IIB                10                 19
  STAGE III                 8                 17
  STAGE IIIA                4                  8
  STAGE IIIB                5                  5
  STAGE IIIC                2                  5
  STAGE IV                  3                  2
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  15Q LOSS MUTATED      11  8 30  0
  15Q LOSS WILD-TYPE    20 28 55  5
D68V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1               11                 20
  T2                   8                 28
  T3                  30                 55
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  15Q LOSS MUTATED   19 22  5  2
  15Q LOSS WILD-TYPE 52 42  7  6
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               19                 52
  N1               22                 42
  N2                5                  7
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   38  5
  15Q LOSS WILD-TYPE 88  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     38    5
  15Q LOSS WILD-TYPE   88    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               38                 88
  1                5                  4
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     6  45
  15Q LOSS WILD-TYPE  18 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6   45
  15Q LOSS WILD-TYPE   18  104
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                6                 18
  MALE                 45                104
[1] 2 2
[1] FALSE
D68V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED      10                         0    36
  15Q LOSS WILD-TYPE    31                         2    75
D68V9, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                   10                 31
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   36                 75
[1] 3 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, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    0 23
  15Q LOSS WILD-TYPE  3 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   23
  15Q LOSS WILD-TYPE    3   58
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               23                 58
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   28 24
  16P LOSS WILD-TYPE 72 47
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                52                119 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                24                 47 
$`16P LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3YC 
        7.63         5.92        13.94         8.94        32.45        20.12 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OE 
       42.77        25.41        23.18        25.22         3.16        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        4.70        32.61        21.01         3.16        58.59         4.90 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NN 
        0.36         7.40         3.95         3.02        12.92         5.49 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        46.09        10.45        12.43        13.41 
TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A7HW TCGA-Q9-A6FU TCGA-R6-A6DN 
        0.10        22.39        12.33        12.00         5.16         8.02 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP 
        7.00         5.29         3.42         4.80         9.27        19.96 
TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-Z6-A8JE TCGA-Z6-AAPN 
       22.82        42.87         2.10         2.66 

$`16P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30        58.55        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.50        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        21.70        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI 
       30.25         0.30         4.31         8.94         3.68        19.99 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU 
       47.93        18.35         3.32         7.17         1.38        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        35.97        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76        21.37         8.71        13.41        27.12 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.36         5.92        12.66         0.10        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59         0.10        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13        33.11         7.82         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV 
        7.04        29.59        15.78        20.02        20.38        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        4.44        18.81        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        30.71        18.18        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-ZR-A9CJ 
        9.17        15.91        10.16         3.42        19.73 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               0.1                0.1 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             83.24             122.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             9.875             12.820 
[1] "0.1 - 83.2 (9.9)"   "0.1 - 122.1 (12.8)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         4        1        2        0        10         7
  16P LOSS WILD-TYPE       4        4        5        1        29        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           6          4          4          0        2
  16P LOSS WILD-TYPE        19          8          6          7        3
                    vv
clus                 STAGE IVA
  16P LOSS MUTATED           0
  16P LOSS WILD-TYPE         4
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  4
  STAGE IB                  2                  5
  STAGE II                  0                  1
  STAGE IIA                10                 29
  STAGE IIB                 7                 22
  STAGE III                 6                 19
  STAGE IIIA                4                  8
  STAGE IIIB                4                  6
  STAGE IIIC                0                  7
  STAGE IV                  2                  3
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  16P LOSS MUTATED      12  9 22  0
  16P LOSS WILD-TYPE    19 27 63  5
D69V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1               12                 19
  T2                   9                 27
  T3                  22                 63
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16P LOSS MUTATED   18 21  4  0
  16P LOSS WILD-TYPE 53 43  8  8
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               18                 53
  N1               21                 43
  N2                4                  8
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   37  2
  16P LOSS WILD-TYPE 89  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     37    2
  16P LOSS WILD-TYPE   89    7
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               37                 89
  1                2                  7
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7  46
  16P LOSS WILD-TYPE  17 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7   46
  16P LOSS WILD-TYPE   17  103
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                7                 17
  MALE                 46                103
[1] 2 2
[1] FALSE
D69V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       9                         1    37
  16P LOSS WILD-TYPE    32                         1    74
D69V9, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    9                 32
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   37                 74
[1] 3 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, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3 21
  16P LOSS WILD-TYPE  0 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   21
  16P LOSS WILD-TYPE    0   60
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO               21                 60
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   29 21
  16Q LOSS WILD-TYPE 71 50
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                50                121 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                21                 50 
$`16Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       31.27         7.63         5.92         8.94        16.24        32.45 
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
       20.09        20.12        14.50        42.77        25.41        23.18 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16         8.94        24.00         4.70        32.61        21.01 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        3.16        58.59         4.90         0.36         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       55.50         5.49         8.71        83.24        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-Q9-A6FU 
       10.45        13.41         0.10        12.33        10.52         5.16 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.06         6.35        53.95         9.30         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP 
       12.69         7.00         5.29         4.80         9.27        19.96 
TCGA-VR-A8EQ TCGA-Z6-AAPN 
       22.82         2.66 

$`16Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       25.78        14.30        58.55        13.94         4.21         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 
        6.21        33.27         0.85        20.78         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        4.31         3.68        19.99        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         1.38        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG 
        8.71         2.60        25.12         7.40         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M 
       21.37        13.41        27.12        52.57         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.43         0.10        13.15        15.35        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        11.54        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       29.59        15.78        20.02        20.38         3.42        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        4.44        18.81        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-ZR-A9CJ 
       19.73 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               0.1                0.1 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             83.24             122.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              9.83              12.82 
[1] "0.1 - 83.2 (9.8)"   "0.1 - 122.1 (12.8)"
[1] "hr=" "1"  
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         4        1        2        0         8         7
  16Q LOSS WILD-TYPE       4        4        5        1        31        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           7          1          4          1        1
  16Q LOSS WILD-TYPE        18         11          6          6        4
                    vv
clus                 STAGE IVA
  16Q LOSS MUTATED           1
  16Q LOSS WILD-TYPE         3
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  4
  STAGE IB                  2                  5
  STAGE II                  0                  1
  STAGE IIA                 8                 31
  STAGE IIB                 7                 22
  STAGE III                 7                 18
  STAGE IIIA                1                 11
  STAGE IIIB                4                  6
  STAGE IIIC                1                  6
  STAGE IV                  1                  4
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  16Q LOSS MUTATED      10  7 24  0
  16Q LOSS WILD-TYPE    21 29 61  5
D70V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               10                 21
  T2                   7                 29
  T3                  24                 61
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16Q LOSS MUTATED   16 18  5  1
  16Q LOSS WILD-TYPE 55 46  7  7
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               16                 55
  N1               18                 46
  N2                5                  7
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   33  2
  16Q LOSS WILD-TYPE 93  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     33    2
  16Q LOSS WILD-TYPE   93    7
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               33                 93
  1                2                  7
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     8  42
  16Q LOSS WILD-TYPE  16 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8   42
  16Q LOSS WILD-TYPE   16  107
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                8                 16
  MALE                 42                107
[1] 2 2
[1] FALSE
D70V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       7                         0    34
  16Q LOSS WILD-TYPE    34                         2    77
D70V9, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    7                 34
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   34                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3 19
  16Q LOSS WILD-TYPE  0 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   19
  16Q LOSS WILD-TYPE    0   62
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO               19                 62
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   40 28
  17P LOSS WILD-TYPE 60 43
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                68                103 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                28                 43 
$`17P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78         7.63         5.92         8.94         4.21        32.45 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6F8 
       18.64         3.88         0.79        23.41        14.50       122.10 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.41        31.56        30.25        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OW 
        4.70        32.61         3.32         7.17         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NL 
        7.43         2.60         0.36         3.95        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49K 
        5.49         8.71        13.41        27.12        83.24         5.92 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A7HV 
       10.45        13.15        13.25        12.59        12.33        10.52 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 
       13.18        33.11         5.16         7.82         7.59         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       29.59         9.30        15.78         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
       20.02         4.80        15.35         9.27         4.44        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
       22.82        12.43         8.12        18.18        42.87        11.24 
TCGA-X8-AAAR TCGA-Z6-AAPN 
       10.16         2.66 

$`17P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE 
       31.27        14.30        58.55        13.94        16.24         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.12         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         4.67        12.16        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        21.70        23.18        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
        6.28         3.16         0.30         4.31         8.94        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        47.93        18.35         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       29.00         6.94         8.71        25.12         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       55.50         2.66        35.97        12.92        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M 
        7.76        21.37        52.57        46.09        10.36        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.43        13.41         0.10        15.35         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.00        12.23        12.03         0.13         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-A7RB 
       14.70         6.35        53.95         2.89        20.38         5.29 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY 
        3.42        18.81         1.55        18.31        28.11        30.71 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       46.19        15.06         9.17        15.91         3.42         2.10 
TCGA-ZR-A9CJ 
       19.73 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.36               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            122.10              68.02 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.88              12.82 
[1] "0.4 - 122.1 (10.9)" "0.1 - 68.0 (12.8)" 
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         4        1        2        0        11        12
  17P LOSS WILD-TYPE       4        4        5        1        28        17
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED          13          2          6          3        2
  17P LOSS WILD-TYPE        12         10          4          4        3
                    vv
clus                 STAGE IVA
  17P LOSS MUTATED           1
  17P LOSS WILD-TYPE         3
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  4
  STAGE IB                  2                  5
  STAGE II                  0                  1
  STAGE IIA                11                 28
  STAGE IIB                12                 17
  STAGE III                13                 12
  STAGE IIIA                2                 10
  STAGE IIIB                6                  4
  STAGE IIIC                3                  4
  STAGE IV                  2                  3
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  17P LOSS MUTATED      10 10 39  1
  17P LOSS WILD-TYPE    21 26 46  4
D71V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               10                 21
  T2                  10                 26
  T3                  39                 46
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17P LOSS MUTATED   23 26  6  4
  17P LOSS WILD-TYPE 48 38  6  4
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               23                 48
  N1               26                 38
  N2                6                  6
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   49  3
  17P LOSS WILD-TYPE 77  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     49    3
  17P LOSS WILD-TYPE   77    6
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               49                 77
  1                3                  6
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    9 59
  17P LOSS WILD-TYPE 15 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      9   59
  17P LOSS WILD-TYPE   15   90
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                9                 15
  MALE                 59                 90
[1] 2 2
[1] FALSE
D71V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED      10                         1    47
  17P LOSS WILD-TYPE    31                         1    64
D71V9, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                   10                 31
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   47                 64
[1] 3 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, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    2 27
  17P LOSS WILD-TYPE  1 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2   27
  17P LOSS WILD-TYPE    1   54
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               27                 54
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   13 11
  17Q LOSS WILD-TYPE 87 60
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                147 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                11                 60 
$`17Q LOSS MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
        8.94         4.21         7.69         0.79        23.41        14.50 
TCGA-JY-A938 TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A891 TCGA-LN-A49L TCGA-LN-A4A1 
       25.41         7.13         0.36         3.95        10.45        12.59 
TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASX 
       12.33         5.16         9.30        12.69         4.80         4.44 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-Z6-AAPN 
       22.82        12.43        28.11        42.87        10.16         2.66 

$`17Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       13.94        16.24        32.45         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        4.67        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        42.77        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        6.94         8.71         2.60        25.12         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35         0.10        13.25         0.10        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.23        12.03        13.18         0.13        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        6.35        53.95        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
       20.02        20.38         5.29         3.42        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       18.81        19.96         1.55        18.31         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        3.42         2.10        19.73 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.36               0.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             42.87             122.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              9.73              12.92 
[1] "0.4 - 42.9 (9.7)"   "0.1 - 122.1 (12.9)"
[1] "hr=" "1.7"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0        0        2        0         4         5
  17Q LOSS WILD-TYPE       8        5        5        1        35        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           4          1          1          0        0
  17Q LOSS WILD-TYPE        21         11          9          7        5
                    vv
clus                 STAGE IVA
  17Q LOSS MUTATED           1
  17Q LOSS WILD-TYPE         3
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  2                  5
  STAGE II                  0                  1
  STAGE IIA                 4                 35
  STAGE IIB                 5                 24
  STAGE III                 4                 21
  STAGE IIIA                1                 11
  STAGE IIIB                1                  9
  STAGE IIIC                0                  7
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  17Q LOSS MUTATED       5  3 12  1
  17Q LOSS WILD-TYPE    26 33 73  4
D72V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                5                 26
  T2                   3                 33
  T3                  12                 73
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17Q LOSS MUTATED    8 11  1  0
  17Q LOSS WILD-TYPE 63 53 11  8
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                8                 63
  N1               11                 53
  N2                1                 11
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    18   1
  17Q LOSS WILD-TYPE 108   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     18    1
  17Q LOSS WILD-TYPE  108    8
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               18                108
  1                1                  8
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3  21
  17Q LOSS WILD-TYPE  21 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   21
  17Q LOSS WILD-TYPE   21  128
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                3                 21
  MALE                 21                128
[1] 2 2
[1] FALSE
D72V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       4                         0    15
  17Q LOSS WILD-TYPE    37                         2    96
D72V9, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    4                 37
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   15                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2 12
  17Q LOSS WILD-TYPE  1 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   12
  17Q LOSS WILD-TYPE    1   69
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               12                 69
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   38 28
  18P LOSS WILD-TYPE 62 43
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                66                105 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                28                 43 
$`18P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        14.30         5.92         8.94        16.24        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       33.27         0.85         2.63         0.79        23.41        14.50 
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       44.75        42.77        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16        30.25         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.70        32.61         7.17         7.43         6.94         2.60 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
       16.47        13.55         8.71        52.57        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A4A1 TCGA-LN-A7HY TCGA-Q9-A6FU 
       10.45        12.43        13.41        12.59        12.03         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.82         7.59        29.59         6.35        53.95         9.30 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-VR-A8EP 
        1.45         7.00        20.02         5.29         9.27        19.96 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.31         8.12        10.16         3.42         2.66        19.73 

$`18P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        58.55         7.63        13.94         4.21         7.69 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        6.21        20.09        20.78        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        12.16       122.10        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A4OI 
       41.52        25.41        21.70         6.28         4.31        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W 
       58.59         4.90        29.00         7.13         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        0.36         7.40         3.02        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49M 
       21.37        13.41        27.12        83.24        46.09        12.66 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        10.52        12.00        12.23        13.18         0.13 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 
       33.11         8.02         5.06        14.70         7.04        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        2.89        12.69        20.38         3.42         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX 
        4.44        18.81        22.82        12.43         1.55        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
        9.17        15.91         2.10 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               0.3                0.1 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              55.5              122.1 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             11.24              12.69 
[1] "0.3 - 55.5 (11.2)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         3        1        3        0        11         9
  18P LOSS WILD-TYPE       5        4        4        1        28        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED          11          4          6          3        2
  18P LOSS WILD-TYPE        14          8          4          4        3
                    vv
clus                 STAGE IVA
  18P LOSS MUTATED           2
  18P LOSS WILD-TYPE         2
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  3                  4
  STAGE II                  0                  1
  STAGE IIA                11                 28
  STAGE IIB                 9                 20
  STAGE III                11                 14
  STAGE IIIA                4                  8
  STAGE IIIB                6                  4
  STAGE IIIC                3                  4
  STAGE IV                  2                  3
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18P LOSS MUTATED      11  8 39  1
  18P LOSS WILD-TYPE    20 28 46  4
D73V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               11                 20
  T2                   8                 28
  T3                  39                 46
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18P LOSS MUTATED   22 26  7  3
  18P LOSS WILD-TYPE 49 38  5  5
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               22                 49
  N1               26                 38
  N2                7                  5
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   44  4
  18P LOSS WILD-TYPE 82  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     44    4
  18P LOSS WILD-TYPE   82    5
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               44                 82
  1                4                  5
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   11 56
  18P LOSS WILD-TYPE 13 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     11   56
  18P LOSS WILD-TYPE   13   93
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               11                 13
  MALE                 56                 93
[1] 2 2
[1] FALSE
D73V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED      11                         0    47
  18P LOSS WILD-TYPE    30                         2    64
D73V9, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                   11                 30
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   47                 64
[1] 3 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, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2 28
  18P LOSS WILD-TYPE  1 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   28
  18P LOSS WILD-TYPE    1   53
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               28                 53
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   55 39
  18Q LOSS WILD-TYPE 45 32
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                94                 77 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                39                 32 
$`18Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        31.27        14.30         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
        7.69         0.85         2.63         3.88         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       23.41         9.96        14.50        12.16        44.75        68.02 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         0.30         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
       32.61         3.32         7.17         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        6.94         2.60         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NR 
       35.97        12.92        13.48        16.47        13.55         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        27.12        83.24        52.57        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 
       12.66        12.43        13.41         0.10        13.25        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       22.39         0.10        12.33        13.22         4.47        12.33 
TCGA-LN-A7HX TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.23        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       29.59         6.35        53.95         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EP 
        7.00        20.02         5.29         3.42         9.27        19.96 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       12.43        18.31         8.12        46.19        15.06         9.17 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       10.16         3.42         2.66        19.73 

$`18Q LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RF 
       58.55         7.63         5.92        13.94         4.21         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       33.27        20.09        20.78        20.12        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB 
       17.03        12.82        14.86         4.67       122.10        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J 
        3.68        41.52        21.70         6.28        30.25         4.31 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
       19.99        21.01        47.93        18.35         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
       58.59         7.13         8.71        25.12         0.36         7.40 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-LN-A49K 
       13.22         7.76         5.49        21.37        46.09         5.92 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       13.15        15.35         0.10         0.10        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.76        12.59        15.52        11.54        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.00        12.03        13.18         0.13         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV 
        7.04         9.30        15.78        20.38         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
        4.44        18.81        22.82         1.55        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE 
       18.18        42.87        11.24        15.91         2.10 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               0.1                0.1 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             83.24             122.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             12.33              13.15 
[1] "0.1 - 83.2 (12.3)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         3        1        4        1        18        16
  18Q LOSS WILD-TYPE       5        4        3        0        21        13
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED          13          6          7          5        4
  18Q LOSS WILD-TYPE        12          6          3          2        1
                    vv
clus                 STAGE IVA
  18Q LOSS MUTATED           2
  18Q LOSS WILD-TYPE         2
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  4
  STAGE IB                  4                  3
  STAGE II                  1                  0
  STAGE IIA                18                 21
  STAGE IIB                16                 13
  STAGE III                13                 12
  STAGE IIIA                6                  6
  STAGE IIIB                7                  3
  STAGE IIIC                5                  2
  STAGE IV                  4                  1
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18Q LOSS MUTATED      14 18 50  2
  18Q LOSS WILD-TYPE    17 18 35  3
D74V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               14                 17
  T2                  18                 18
  T3                  50                 35
  T4                   2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18Q LOSS MUTATED   33 36  9  5
  18Q LOSS WILD-TYPE 38 28  3  3
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               33                 38
  N1               36                 28
  N2                9                  3
  N3                5                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   67  6
  18Q LOSS WILD-TYPE 59  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     67    6
  18Q LOSS WILD-TYPE   59    3
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               67                 59
  1                6                  3
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   13 82
  18Q LOSS WILD-TYPE 11 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     13   82
  18Q LOSS WILD-TYPE   11   67
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               13                 11
  MALE                 82                 67
[1] 2 2
[1] FALSE
D74V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED      21                         1    61
  18Q LOSS WILD-TYPE    20                         1    50
D74V9, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                   21                 20
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   61                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2 42
  18Q LOSS WILD-TYPE  1 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   42
  18Q LOSS WILD-TYPE    1   39
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               42                 39
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED   35 25
  19P LOSS WILD-TYPE 65 46
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                60                111 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                25                 46 
$`19P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30         7.63        16.24         4.21 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
        2.63         3.88         0.53        17.03        23.41         9.96 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43J 
       14.50       122.10        68.02        42.77        30.25         4.31 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88V 
        3.68        47.93         7.17        58.59         7.43         2.60 
TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
        3.95         2.66        16.47        13.55        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
        8.71        52.57        46.09        10.45        12.66         0.10 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       15.35        13.25        12.46        12.59        12.49        12.76 
TCGA-LN-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-R6-A6DN 
        0.10         4.47        12.33        12.23        13.18         8.02 
TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EW 
        7.04        15.78         3.42         9.27        18.81         8.12 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.18        42.87        46.19         9.17         2.66        19.73 

$`19P LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE 
       58.55         5.92        13.94         8.94        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        6.21        33.27        20.09         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       18.64         9.30         0.79        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       12.16        44.75        60.39         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
        3.16         0.30         8.94        24.00         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       19.99        21.01        18.35         3.32         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        4.90        29.00         7.13         6.94         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40         3.02        55.50        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.48         7.76        21.37        13.41        27.12        83.24 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V 
       10.36         5.92        12.43        13.41        13.15         0.10 
TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10        12.59        22.39        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO 
       13.22        25.25        10.52        12.00        12.03         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         5.16         7.82         7.59         5.06        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
       29.59         6.35        53.95         9.30         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       12.69         7.00        20.02        20.38         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         4.44        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I 
       18.31        28.11        30.71        15.06        11.24        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       10.16         3.42         2.10 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               0.1                0.1 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            122.10              83.24 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             12.54              12.59 
[1] "0.1 - 122.1 (12.5)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.1"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         2        2        2        1        13        11
  19P LOSS WILD-TYPE       6        3        5        0        26        18
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED          12          3          3          3        1
  19P LOSS WILD-TYPE        13          9          7          4        4
                    vv
clus                 STAGE IVA
  19P LOSS MUTATED           3
  19P LOSS WILD-TYPE         1
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  2                  3
  STAGE IB                  2                  5
  STAGE II                  1                  0
  STAGE IIA                13                 26
  STAGE IIB                11                 18
  STAGE III                12                 13
  STAGE IIIA                3                  9
  STAGE IIIB                3                  7
  STAGE IIIC                3                  4
  STAGE IV                  1                  4
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  19P LOSS MUTATED       9 12 36  0
  19P LOSS WILD-TYPE    22 24 49  5
D75V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1                9                 22
  T2                  12                 24
  T3                  36                 49
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19P LOSS MUTATED   21 30  2  3
  19P LOSS WILD-TYPE 50 34 10  5
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               21                 50
  N1               30                 34
  N2                2                 10
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   47  4
  19P LOSS WILD-TYPE 79  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     47    4
  19P LOSS WILD-TYPE   79    5
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               47                 79
  1                4                  5
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    7 54
  19P LOSS WILD-TYPE 17 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7   54
  19P LOSS WILD-TYPE   17   95
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                7                 17
  MALE                 54                 95
[1] 2 2
[1] FALSE
D75V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED      19                         1    33
  19P LOSS WILD-TYPE    22                         1    78
D75V9, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                   19                 22
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   33                 78
[1] 3 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, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    0 28
  19P LOSS WILD-TYPE  3 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   28
  19P LOSS WILD-TYPE    3   53
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               28                 53
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED   29 18
  19Q LOSS WILD-TYPE 71 53
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                47                124 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                18                 53 
$`19Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A50L 
       25.78        31.27        14.30         4.21         2.63         0.53 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH 
       23.41         9.96        14.50       122.10        68.02        42.77 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX 
       30.25         4.31        47.93         7.17        58.59         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NR 
        6.94         2.60         3.95         2.66        13.22         8.71 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y 
       10.45        12.66         0.10        13.15        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.59        12.49         4.47        12.33        12.23        13.18 
TCGA-R6-A6DN TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EW 
        8.02        15.78         1.45         3.42        18.81         8.12 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.18        42.87         9.17         2.66        19.73 

$`19Q LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       32.45         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       20.78        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        12.82        14.86         4.67        12.16        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       60.39         3.68        41.52        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       21.01        18.35         3.32         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
       29.00         7.13         8.71        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
       13.55         7.76         5.49        21.37        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       83.24        52.57        46.09        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.41        15.35         0.10         0.10        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       25.25        10.52        12.00        12.03         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WG 
       29.59         6.35        53.95         9.30         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.02        20.38         5.29         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       18.31        28.11        30.71        46.19        15.06        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        10.16         3.42         2.10 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               0.1                0.1 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            122.10              83.24 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            12.460             12.725 
[1] "0.1 - 122.1 (12.5)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         2        2        1        0        11         9
  19Q LOSS WILD-TYPE       6        3        6        1        28        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           8          3          2          3        1
  19Q LOSS WILD-TYPE        17          9          8          4        4
                    vv
clus                 STAGE IVA
  19Q LOSS MUTATED           2
  19Q LOSS WILD-TYPE         2
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  2                  3
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                11                 28
  STAGE IIB                 9                 20
  STAGE III                 8                 17
  STAGE IIIA                3                  9
  STAGE IIIB                2                  8
  STAGE IIIC                3                  4
  STAGE IV                  1                  4
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  19Q LOSS MUTATED       6 10 29  0
  19Q LOSS WILD-TYPE    25 26 56  5
D76V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1                6                 25
  T2                  10                 26
  T3                  29                 56
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19Q LOSS MUTATED   19 21  1  3
  19Q LOSS WILD-TYPE 52 43 11  5
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               19                 52
  N1               21                 43
  N2                1                 11
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   36  3
  19Q LOSS WILD-TYPE 90  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     36    3
  19Q LOSS WILD-TYPE   90    6
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               36                 90
  1                3                  6
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     6  42
  19Q LOSS WILD-TYPE  18 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6   42
  19Q LOSS WILD-TYPE   18  107
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                6                 18
  MALE                 42                107
[1] 2 2
[1] FALSE
D76V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED      17                         1    24
  19Q LOSS WILD-TYPE    24                         1    87
D76V9, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                   17                 24
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   24                 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"
D76V10, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    0 23
  19Q LOSS WILD-TYPE  3 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   23
  19Q LOSS WILD-TYPE    3   58
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               23                 58
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED   14  4
  20P LOSS WILD-TYPE 86 67
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                153 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 67 
$`20P LOSS MUTATED`
TCGA-2H-A9GI TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OF 
       14.30        44.75        68.02        42.77         8.94         3.68 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NL TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O 
       32.61         3.32        13.22        83.24        12.66        13.41 
TCGA-LN-A49Y TCGA-LN-A7HW TCGA-LN-A7HY TCGA-R6-A6XG TCGA-S8-A6BW TCGA-VR-A8EQ 
       12.46        12.00        12.03        29.59        20.38        22.82 

$`20P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       12.16       122.10        60.39         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
        3.16        30.25         0.30         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        5.92        10.45        12.43         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.25         0.10        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        14.70         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.02         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       15.06        11.24         9.17        15.91        10.16         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         2.66        19.73 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              3.32               0.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             83.24             122.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            13.855             12.430 
[1] "3.3 - 83.2 (13.9)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "3.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         1        0        1        0         6         3
  20P LOSS WILD-TYPE       7        5        6        1        33        26
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           4          0          0          1        0
  20P LOSS WILD-TYPE        21         12         10          6        5
                    vv
clus                 STAGE IVA
  20P LOSS MUTATED           0
  20P LOSS WILD-TYPE         4
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 6                 33
  STAGE IIB                 3                 26
  STAGE III                 4                 21
  STAGE IIIA                0                 12
  STAGE IIIB                0                 10
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20P LOSS MUTATED       2  6  9  0
  20P LOSS WILD-TYPE    29 30 76  5
D77V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                2                 29
  T2                   6                 30
  T3                   9                 76
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20P LOSS MUTATED    8  7  1  1
  20P LOSS WILD-TYPE 63 57 11  7
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                8                 63
  N1                7                 57
  N2                1                 11
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    14   0
  20P LOSS WILD-TYPE 112   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     14    0
  20P LOSS WILD-TYPE  112    9
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               14                112
  1                0                  9
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  16
  20P LOSS WILD-TYPE  22 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   16
  20P LOSS WILD-TYPE   22  133
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 22
  MALE                 16                133
[1] 2 2
[1] FALSE
D77V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       7                         0     9
  20P LOSS WILD-TYPE    34                         2   102
D77V9, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    7                 34
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    9                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    0  7
  20P LOSS WILD-TYPE  3 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    7
  20P LOSS WILD-TYPE    3   74
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                7                 74
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    5  2
  20Q LOSS WILD-TYPE 95 69
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                164 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 69 
$`20Q LOSS MUTATED`
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OO TCGA-LN-A7HW TCGA-S8-A6BW 
       44.75        42.77         8.94         3.32        12.00        20.38 
TCGA-VR-A8EQ 
       22.82 

$`20Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
        5.92        10.45        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35         0.10        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        10.52        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       33.11         5.16         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       15.78         2.89         1.45        12.69         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        19.96        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              3.32               0.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             44.75             122.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             20.38              12.54 
[1] "3.3 - 44.8 (20.4)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.9"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0        0        1        0         1         3
  20Q LOSS WILD-TYPE       8        5        6        1        38        26
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           1          0          0          1        0
  20Q LOSS WILD-TYPE        24         12         10          6        5
                    vv
clus                 STAGE IVA
  20Q LOSS MUTATED           0
  20Q LOSS WILD-TYPE         4
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  1                  6
  STAGE II                  0                  1
  STAGE IIA                 1                 38
  STAGE IIB                 3                 26
  STAGE III                 1                 24
  STAGE IIIA                0                 12
  STAGE IIIB                0                 10
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20Q LOSS MUTATED       0  5  3  0
  20Q LOSS WILD-TYPE    31 31 82  5
D78V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                0                 31
  T2                   5                 31
  T3                   3                 82
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20Q LOSS MUTATED    2  4  1  1
  20Q LOSS WILD-TYPE 69 60 11  7
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                2                 69
  N1                4                 60
  N2                1                 11
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   0
  20Q LOSS WILD-TYPE 120   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  120    9
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                6                120
  1                0                  9
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   7
  20Q LOSS WILD-TYPE  23 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    7
  20Q LOSS WILD-TYPE   23  142
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 23
  MALE                  7                142
[1] 2 2
[1] FALSE
D78V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       3                         0     4
  20Q LOSS WILD-TYPE    38                         2   107
D78V9, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    3                 38
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    4                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  3
  20Q LOSS WILD-TYPE  3 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    3
  20Q LOSS WILD-TYPE    3   78
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                3                 78
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   55 43
  21Q LOSS WILD-TYPE 45 28
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                98                 73 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                43                 28 
$`21Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR 
       25.78         7.63         5.92        13.94         8.94        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A93C TCGA-JY-A93D 
        0.53         0.79         9.96       122.10        23.18        31.56 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       24.03         3.16        30.25         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP 
       24.00         4.70        32.61        21.01        47.93         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        6.94         2.60         0.36         7.40         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR 
        2.66        12.92        16.47        13.55        13.22         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        52.57        46.09        10.36         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A3 
       12.43        13.41         0.10        13.15        13.25        12.76 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX 
        0.10        12.33        13.22        12.33        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        13.18        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06         7.04        29.59         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        2.89         1.45        12.69         4.80         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
       18.81        22.82        12.43         1.55         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JE 
       18.18        42.87        46.19        11.24         9.17         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`21Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        14.30        58.55        16.24         4.21         7.69 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
        6.21        20.09         2.63         9.30        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON 
       21.70        25.22         6.28         3.68        19.99        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NG 
        3.32         1.38         8.71        25.12        55.50        35.97 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L 
       13.48         7.76         5.49        21.37        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       12.66        15.35         0.10         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 
       12.49        12.59        22.39        15.52        11.54         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A9FO TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 
       25.25        10.52         0.13        14.70        53.95        15.78 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        7.00        20.02        20.38         5.29         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR 
       19.96        18.31        30.71        15.06        15.91        10.16 
TCGA-Z6-A8JD 
        3.42 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               0.1                0.1 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            122.10              83.24 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             11.62              14.70 
[1] "0.1 - 122.1 (11.6)" "0.1 - 83.2 (14.7)" 
[1] "hr=" "1.4"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         6        3        6        1        16        12
  21Q LOSS WILD-TYPE       2        2        1        0        23        17
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED          16          6          7          5        3
  21Q LOSS WILD-TYPE         9          6          3          2        2
                    vv
clus                 STAGE IVA
  21Q LOSS MUTATED           2
  21Q LOSS WILD-TYPE         2
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   6                  2
  STAGE IA                  3                  2
  STAGE IB                  6                  1
  STAGE II                  1                  0
  STAGE IIA                16                 23
  STAGE IIB                12                 17
  STAGE III                16                  9
  STAGE IIIA                6                  6
  STAGE IIIB                7                  3
  STAGE IIIC                5                  2
  STAGE IV                  3                  2
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  21Q LOSS MUTATED      17 17 49  3
  21Q LOSS WILD-TYPE    14 19 36  2
D79V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               17                 14
  T2                  17                 19
  T3                  49                 36
  T4                   3                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  21Q LOSS MUTATED   38 35  7  6
  21Q LOSS WILD-TYPE 33 29  5  2
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               38                 33
  N1               35                 29
  N2                7                  5
  N3                6                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   70  5
  21Q LOSS WILD-TYPE 56  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     70    5
  21Q LOSS WILD-TYPE   56    4
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               70                 56
  1                5                  4
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   16 83
  21Q LOSS WILD-TYPE  8 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     16   83
  21Q LOSS WILD-TYPE    8   66
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               16                  8
  MALE                 83                 66
[1] 2 2
[1] FALSE
D79V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED      19                         0    67
  21Q LOSS WILD-TYPE    22                         2    44
D79V9, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                   19                 22
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   67                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    2 41
  21Q LOSS WILD-TYPE  1 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   41
  21Q LOSS WILD-TYPE    1   40
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               41                 40
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   36 34
  22Q LOSS WILD-TYPE 64 37
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                70                101 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                34                 37 
$`22Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YB TCGA-IG-A4P3 
        8.94        16.24         4.21        32.45         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6F8 
        3.88         0.53         0.79        23.41         4.67       122.10 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OG 
       42.77        25.41        31.56         3.16        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88Y 
       32.61        58.59         4.90        29.00         7.13         0.36 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW 
       16.47        13.55        13.22         5.49         8.71        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.36         5.92        10.45        13.41         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.25         0.10        12.76        10.52        12.03        13.18 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8W8 
        8.02         7.59         5.06        29.59        15.78         2.89 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ 
        7.00         5.29         4.80         9.27        18.81        22.82 
TCGA-VR-A8EU TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.31         2.10         2.66        19.73 

$`22Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       25.78         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.78        20.12         9.30        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86        14.50        12.16        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        21.70        23.18        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF 
        6.28        30.25         0.30         4.31         8.94         3.68 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        1.38         3.16         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS 
       25.12         3.95        35.97         7.76        21.37        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S 
       27.12        83.24        52.57        12.66        12.43        13.15 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.46        12.59        12.49        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 
       12.33        25.25        12.00        12.23         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.16         7.82        14.70         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC 
        9.30         1.45        12.69        20.02        20.38         3.42 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       15.35         4.44        19.96        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       11.24         9.17        15.91        10.16         3.42 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               0.1                0.1 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            122.10              83.24 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            11.275             12.590 
[1] "0.1 - 122.1 (11.3)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.4"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         5        0        3        0        12        10
  22Q LOSS WILD-TYPE       3        5        4        1        27        19
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED          15          3          4          3        3
  22Q LOSS WILD-TYPE        10          9          6          4        2
                    vv
clus                 STAGE IVA
  22Q LOSS MUTATED           3
  22Q LOSS WILD-TYPE         1
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   5                  3
  STAGE IA                  0                  5
  STAGE IB                  3                  4
  STAGE II                  0                  1
  STAGE IIA                12                 27
  STAGE IIB                10                 19
  STAGE III                15                 10
  STAGE IIIA                3                  9
  STAGE IIIB                4                  6
  STAGE IIIC                3                  4
  STAGE IV                  3                  2
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  22Q LOSS MUTATED      15 10 38  0
  22Q LOSS WILD-TYPE    16 26 47  5
D80V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1               15                 16
  T2                  10                 26
  T3                  38                 47
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  22Q LOSS MUTATED   24 33  3  3
  22Q LOSS WILD-TYPE 47 31  9  5
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               24                 47
  N1               33                 31
  N2                3                  9
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   52  6
  22Q LOSS WILD-TYPE 74  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     52    6
  22Q LOSS WILD-TYPE   74    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               52                 74
  1                6                  3
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   10 60
  22Q LOSS WILD-TYPE 14 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   60
  22Q LOSS WILD-TYPE   14   89
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               10                 14
  MALE                 60                 89
[1] 2 2
[1] FALSE
D80V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED      13                         0    44
  22Q LOSS WILD-TYPE    28                         2    67
D80V9, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                   13                 28
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   44                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    1 30
  22Q LOSS WILD-TYPE  2 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   30
  22Q LOSS WILD-TYPE    2   51
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               30                 51
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED   33 22
  XP LOSS WILD-TYPE 67 49
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               55               116 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               22                49 
$`XP LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YA 
       25.78        14.30         4.21        32.45        20.09        20.78 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        3.88         0.53        23.41        12.82         9.96         4.67 
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OE 
       44.75        42.77        25.41        23.18        30.25        24.00 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ 
       21.01        18.35         7.17         3.95        13.48        16.47 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R 
        8.71        13.41        46.09         5.92        12.66         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 
       12.46        12.59        22.39        11.54        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ 
       10.52        12.00         0.13        33.11         8.02         5.06 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        1.45        12.69        20.02         4.80         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-Z6-A8JD 
       18.81        18.31         8.12        42.87        15.91         3.42 
TCGA-Z6-A8JE 
        2.10 

$`XP LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB 
       16.24         7.69         6.21        33.27         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A7DP 
       20.12        18.64         9.30        17.03         0.79        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         0.30         4.31         8.94         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       32.61        19.99        47.93         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
        8.71         2.60        25.12         0.36         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        35.97        12.92        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        27.12        83.24        52.57 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.36        10.45        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        13.25         0.10        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
        0.10        15.52        12.33         4.47        12.33        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.03        13.18         5.16         7.82         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        2.89         7.00        20.38         5.29         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        22.82        12.43         1.55        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       18.18        46.19        15.06        11.24         9.17        10.16 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
              0.1               0.1 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            46.09            122.10 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            12.82             12.38 
[1] "0.1 - 46.1 (12.8)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1"  
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         2        1        2        0        14        10
  XP LOSS WILD-TYPE       6        4        5        1        25        19
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           8          5          7          0        1
  XP LOSS WILD-TYPE        17          7          3          7        4
                   vv
clus                STAGE IVA
  XP LOSS MUTATED           0
  XP LOSS WILD-TYPE         4
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 1                 4
  STAGE IB                 2                 5
  STAGE II                 0                 1
  STAGE IIA               14                25
  STAGE IIB               10                19
  STAGE III                8                17
  STAGE IIIA               5                 7
  STAGE IIIB               7                 3
  STAGE IIIC               0                 7
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  XP LOSS MUTATED       6 13 30  2
  XP LOSS WILD-TYPE    25 23 55  3
D81V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1               6                25
  T2                 13                23
  T3                 30                55
  T4                  2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  XP LOSS MUTATED   26 19  6  0
  XP LOSS WILD-TYPE 45 45  6  8
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              26                45
  N1              19                45
  N2               6                 6
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   46  1
  XP LOSS WILD-TYPE 80  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     46    1
  XP LOSS WILD-TYPE   80    8
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              46                80
  1               1                 8
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    4 53
  XP LOSS WILD-TYPE 20 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      4   53
  XP LOSS WILD-TYPE   20   96
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               4                20
  MALE                53                96
[1] 2 2
[1] FALSE
D81V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED      20                         0    31
  XP LOSS WILD-TYPE    21                         2    80
D81V9, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                  20                21
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  31                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    1 31
  XP LOSS WILD-TYPE  2 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1   31
  XP LOSS WILD-TYPE    2   50
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              31                50
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   23 15
  XQ LOSS WILD-TYPE 77 56
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               38               133 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                56 
$`XQ LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A625 TCGA-JY-A6FH TCGA-JY-A938 
       25.78         4.21        32.45        12.82        42.77        25.41 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
       30.25        24.00        21.01        18.35         7.17         3.16 
TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NW TCGA-LN-A49R 
        3.95        13.48        16.47         8.71        46.09         0.10 
TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.46        22.39        11.54        13.22        25.25        10.52 
TCGA-LN-A7HW TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A8WC TCGA-R6-A8WG 
       12.00        33.11         8.02         5.06         1.45        12.69 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8Q7 
        3.42         4.80         9.27         4.44        18.81        42.87 
TCGA-Z6-A8JD TCGA-Z6-A8JE 
        3.42         2.10 

$`XQ LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       60.39        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        4.31         8.94         3.68         4.70        32.61        19.99 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93         3.32         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.25         0.10        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.59         0.10        15.52        12.33         4.47        12.33 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.23        12.03        13.18         0.13         5.16         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        9.30        15.78         2.89         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        5.29        15.35        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        30.71        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-AAPN 
       15.06        11.24         9.17        15.91        10.16         2.66 
TCGA-ZR-A9CJ 
       19.73 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              0.1               0.1 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            46.09            122.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           12.575            12.590 
[1] "0.1 - 46.1 (12.6)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1"  
D82V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         2        2        2        0        10         4
  XQ LOSS WILD-TYPE       6        3        5        1        29        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           6          2          3          0        0
  XQ LOSS WILD-TYPE        19         10          7          7        5
                   vv
clus                STAGE IVA
  XQ LOSS MUTATED           0
  XQ LOSS WILD-TYPE         4
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 3
  STAGE IB                 2                 5
  STAGE II                 0                 1
  STAGE IIA               10                29
  STAGE IIB                4                25
  STAGE III                6                19
  STAGE IIIA               2                10
  STAGE IIIB               3                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 5
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  XQ LOSS MUTATED       6  8 18  0
  XQ LOSS WILD-TYPE    25 28 67  5
D82V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1               6                25
  T2                  8                28
  T3                 18                67
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  XQ LOSS MUTATED   18 12  2  0
  XQ LOSS WILD-TYPE 53 52 10  8
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              18                53
  N1              12                52
  N2               2                10
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   28  0
  XQ LOSS WILD-TYPE 98  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     28    0
  XQ LOSS WILD-TYPE   98    9
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              28                98
  1               0                 9
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3  36
  XQ LOSS WILD-TYPE  21 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   36
  XQ LOSS WILD-TYPE   21  113
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                21
  MALE                36               113
[1] 2 2
[1] FALSE
D82V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED      10                         1    23
  XQ LOSS WILD-TYPE    31                         1    88
D82V9, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                  10                31
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  23                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V10, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1 19
  XQ LOSS WILD-TYPE  2 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   19
  XQ LOSS WILD-TYPE    2   62
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              19                62
[1] 2 2
[1] FALSE
