[1] "ofn"       "-oTACC-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/ACC-TP/22489368/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/22522856/transformed.cor.cli.txt"

nPatients in clinical file=92, in cluster file=90, common to both=90
[1] 82 90
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                86 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                86 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                82 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                82 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13                77 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13                77 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13                77 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13                77 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               14                76 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               14                76 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16                74 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16                74 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               38                52 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               38                52 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               35                55 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               35                55 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               57                33 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               57                33 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               55                35 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               55                35 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               18                72 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               18                72 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                74 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                74 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               48                42 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               48                42 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48                42 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48                42 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32                58 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32                58 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               38                52 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               38                52 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               21                69 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               21                69 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               27                63 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               27                63 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                25                 65 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                25                 65 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                 64 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                 64 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 85 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 85 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 84 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 84 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                64                 26 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                64                 26 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                64                 26 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                64                 26 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 84 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 84 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 69 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 69 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 79 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 79 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                50                 40 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                50                 40 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                47                 43 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                47                 43 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 85 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 85 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 83 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 83 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 84 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 84 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 85 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 85 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                 34 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                 34 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                52                 38 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                52                 38 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                46                 44 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                46                 44 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                49                 41 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                49                 41 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                 59 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                 59 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 87 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 87 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               43                47 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               43                47 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               41                49 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               41                49 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               29                61 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               29                61 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21                69 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21                69 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16                74 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16                74 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14                76 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14                76 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               19                71 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               19                71 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19                71 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19                71 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                81 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                81 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                80 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                80 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                83 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                83 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5                85 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5                85 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19                71 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19                71 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                68 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                68 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                85 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                85 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                84 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                84 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                74 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                74 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12                78 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12                78 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20                70 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20                70 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12                78 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12                78 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                 78 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                 78 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 80 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 80 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                23                 67 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                23                 67 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 68 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 68 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 85 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 85 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 86 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 86 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                39                 51 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                39                 51 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 72 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 72 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                 69 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                 69 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 86 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 86 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 85 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 85 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                33                 57 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                33                 57 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                 65 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                 65 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 53 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 53 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                35                 55 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                35                 55 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 85 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 85 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 86 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 86 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 81 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 81 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 87 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 87 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 75 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 75 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                48                 42 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                48                 42 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               16                74 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               16                74 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16                74 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16                74 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 90 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=32,	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=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 90 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "GENDER"                "RADIATION_THERAPY"    
 [7] "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"        "NUMBER_OF_LYMPH_NODES"
[10] "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=50, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 9 48 11 20 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 9 48 11 20 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
 9 48 11 20 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 9 48 11 20 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=7, 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    2  2
  1P GAIN WILD-TYPE 55 31
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                86 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                31 
$`1P GAIN MUTATED`
TCGA-P6-A5OG TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-PK-A5HC 
       12.59        11.31        24.36        22.32 

$`1P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        30.31        18.12        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        67.59        18.48        39.25        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ 
       35.57        16.37        49.08        24.62        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        29.10        28.64        23.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       21.76        14.63        52.24        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       90.08        53.03        61.08        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG 
       28.04        36.03        18.05        38.50         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            11.31              0.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            24.36            153.63 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           17.455            39.415 
[1] "11.3 - 24.4 (17.5)" "0.0 - 153.6 (39.4)"
[1] "hr=" "3.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         0        2         1        1
  1P GAIN WILD-TYPE       9       41        17       17
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0                 9
  STAGE II                2                41
  STAGE III               1                17
  STAGE IV                1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1P GAIN MUTATED    0  2  0  2
  1P GAIN WILD-TYPE  9 46 11 18
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               0                 9
  T2               2                46
  T3               0                11
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4  0
  1P GAIN WILD-TYPE 74 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    0
  1P GAIN WILD-TYPE   74   10
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               4                74
  1               0                10
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4  0
  1P GAIN WILD-TYPE 55 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    0
  1P GAIN WILD-TYPE   55   31
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               4                55
  MALE                 0                31
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4  0
  1P GAIN WILD-TYPE 65 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    0
  1P GAIN WILD-TYPE   65   18
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                4                65
  YES               0                18
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  1P GAIN MUTATED                                       0
  1P GAIN WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  1P GAIN MUTATED                                          0
  1P GAIN WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  1P GAIN MUTATED                                      4
  1P GAIN WILD-TYPE                                   81
D1V8, multiclass
                                          clus
vv                                         1P GAIN MUTATED 1P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   4                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  1P GAIN MUTATED    2  1  1  0
  1P GAIN WILD-TYPE 61  6 11  5
D1V9, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               2                61
  R1               1                 6
  R2               1                11
  RX               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"
D1V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         0     3
  1P GAIN WILD-TYPE     1                         1    73
D1V11, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    0  3
  1P GAIN WILD-TYPE  8 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    3
  1P GAIN WILD-TYPE    8   35
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               3                35
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    3  5
  1Q GAIN WILD-TYPE 54 28
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                82 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                28 
$`1Q GAIN MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5JE TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB 
       12.59        55.13        69.21        16.37        11.31        24.36 
TCGA-OR-A5LS TCGA-PK-A5HC 
       36.03        22.32 

$`1Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       44.45        30.31        18.12        57.53        99.88        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        69.37        76.64        16.11        49.22        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       18.48        39.25        15.25        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 
       27.02       108.13        32.68       113.92        35.57        49.08 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.62        46.49        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        68.25        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       60.89       152.15        31.79        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       23.64         5.23        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       78.41        14.33        36.33        90.08        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI 
       77.00        79.07        61.05        28.04        18.05        38.50 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
        0.00        24.85        20.25        39.48 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            11.31              0.00 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            69.21            153.63 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           23.340            39.415 
[1] "11.3 - 69.2 (23.3)" "0.0 - 153.6 (39.4)"
[1] "hr=" "2.6"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         1        3         2        2
  1Q GAIN WILD-TYPE       8       40        16       16
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                3                40
  STAGE III               2                16
  STAGE IV                2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    1  3  2  2
  1Q GAIN WILD-TYPE  8 45  9 18
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               1                 8
  T2               3                45
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    8  0
  1Q GAIN WILD-TYPE 70 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8    0
  1Q GAIN WILD-TYPE   70   10
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               8                70
  1               0                10
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    8  0
  1Q GAIN WILD-TYPE 51 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8    0
  1Q GAIN WILD-TYPE   51   31
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               8                51
  MALE                 0                31
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    7  1
  1Q GAIN WILD-TYPE 62 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7    1
  1Q GAIN WILD-TYPE   62   17
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                7                62
  YES               1                17
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  1Q GAIN MUTATED                                       0
  1Q GAIN WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  1Q GAIN MUTATED                                          0
  1Q GAIN WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  1Q GAIN MUTATED                                      8
  1Q GAIN WILD-TYPE                                   77
D2V8, multiclass
                                          clus
vv                                         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   8                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"
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED    5  1  2  0
  1Q GAIN WILD-TYPE 58  6 10  5
D2V9, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0               5                58
  R1               1                 6
  R2               2                10
  RX               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"
D2V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         0     6
  1Q GAIN WILD-TYPE     1                         1    70
D2V11, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   6                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"
D2V12, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    1  3
  1Q GAIN WILD-TYPE  7 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1    3
  1Q GAIN WILD-TYPE    7   35
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               3                35
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    3 10
  2P GAIN WILD-TYPE 54 23
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13                77 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                23 
$`2P GAIN MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JM TCGA-OR-A5JP 
       91.30        88.87        16.11        69.21        18.48        15.25 
TCGA-OR-A5JU TCGA-OR-A5K5 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LL 
        9.50        16.37         5.23        39.35        14.33        53.03 
TCGA-P6-A5OH 
        0.00 

$`2P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        43.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5J9 
       55.13        68.75        13.91        12.00        19.04        44.45 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        18.12        57.53        99.88        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO 
       69.37        76.64        16.11        49.22        67.59        39.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       36.26       121.25        12.59        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       35.57        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       44.84        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE 
       31.79        28.31        29.10        28.64        23.64        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
       14.63        52.24        78.41        36.33        90.08        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       77.00        79.07        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50        24.85        20.25        39.48        22.32 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.00              4.11 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            91.30            153.63 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            16.37             39.48 
[1] "0.0 - 91.3 (16.4)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "3.6"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED         1        4         4        4
  2P GAIN WILD-TYPE       8       39        14       14
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                4                39
  STAGE III               4                14
  STAGE IV                4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    1  4  3  5
  2P GAIN WILD-TYPE  8 44  8 15
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               1                 8
  T2               4                44
  T3               3                 8
  T4               5                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   13  0
  2P GAIN WILD-TYPE 65 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     13    0
  2P GAIN WILD-TYPE   65   10
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              13                65
  1               0                10
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   11  2
  2P GAIN WILD-TYPE 48 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     11    2
  2P GAIN WILD-TYPE   48   29
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              11                48
  MALE                 2                29
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   10  3
  2P GAIN WILD-TYPE 59 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     10    3
  2P GAIN WILD-TYPE   59   15
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               10                59
  YES               3                15
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  2P GAIN MUTATED                                       0
  2P GAIN WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  2P GAIN MUTATED                                          0
  2P GAIN WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  2P GAIN MUTATED                                     13
  2P GAIN WILD-TYPE                                   72
D3V8, multiclass
                                          clus
vv                                         2P GAIN MUTATED 2P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  13                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED    7  2  3  1
  2P GAIN WILD-TYPE 56  5  9  4
D3V9, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               7                56
  R1               2                 5
  R2               3                 9
  RX               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"
D3V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         1    11
  2P GAIN WILD-TYPE     2                         0    65
D3V11, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  11                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    2  5
  2P GAIN WILD-TYPE  6 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    5
  2P GAIN WILD-TYPE    6   33
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               5                33
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    5  8
  2Q GAIN WILD-TYPE 52 25
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13                77 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                25 
$`2Q GAIN MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JP TCGA-OR-A5JU 
       91.30        88.87        16.11        69.21        15.25         9.50 
TCGA-OR-A5K5 TCGA-OR-A5KB TCGA-OR-A5KX TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LI 
       16.37        24.36        44.84         5.23        39.35        14.33 
TCGA-P6-A5OH 
        0.00 

$`2Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        43.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5J9 
       55.13        68.75        13.91        12.00        19.04        44.45 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        18.12        57.53        99.88        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM 
       69.37        76.64        16.11        49.22        67.59        18.48 
TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV 
       39.25        36.26       121.25        12.59        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       72.39        31.23        18.15        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO 
      113.92        35.57        49.08        24.62        11.31        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF 
       28.31        29.10        28.64        23.64        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        36.33        90.08        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       77.00        79.07        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50        24.85        20.25        39.48        22.32 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.00              4.11 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            91.30            153.63 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            16.37             39.48 
[1] "0.0 - 91.3 (16.4)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "2.6"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED         1        4         5        3
  2Q GAIN WILD-TYPE       8       39        13       15
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                4                39
  STAGE III               5                13
  STAGE IV                3                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    1  5  3  4
  2Q GAIN WILD-TYPE  8 43  8 16
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               1                 8
  T2               5                43
  T3               3                 8
  T4               4                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   12  1
  2Q GAIN WILD-TYPE 66  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     12    1
  2Q GAIN WILD-TYPE   66    9
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              12                66
  1               1                 9
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   11  2
  2Q GAIN WILD-TYPE 48 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     11    2
  2Q GAIN WILD-TYPE   48   29
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              11                48
  MALE                 2                29
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   11  2
  2Q GAIN WILD-TYPE 58 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     11    2
  2Q GAIN WILD-TYPE   58   16
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               11                58
  YES               2                16
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  2Q GAIN MUTATED                                       0
  2Q GAIN WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  2Q GAIN MUTATED                                          0
  2Q GAIN WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  2Q GAIN MUTATED                                     13
  2Q GAIN WILD-TYPE                                   72
D4V8, multiclass
                                          clus
vv                                         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  13                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED    8  1  3  1
  2Q GAIN WILD-TYPE 55  6  9  4
D4V9, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               8                55
  R1               1                 6
  R2               3                 9
  RX               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"
D4V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         1    12
  2Q GAIN WILD-TYPE     2                         0    64
D4V11, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  12                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"
D4V12, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2  7
  2Q GAIN WILD-TYPE  6 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    7
  2Q GAIN WILD-TYPE    6   31
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               7                31
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   11  3
  3P GAIN WILD-TYPE 46 30
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               14                76 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                30 
$`3P GAIN MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV 
       12.59        55.13        69.37        36.26       121.25        66.51 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5L2 TCGA-OR-A5L8 TCGA-OR-A5LK 
       24.36        46.49        83.80        60.89        29.10        90.08 
TCGA-OR-A5LT TCGA-OU-A5PI 
       18.05        38.50 

$`3P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       44.45        30.31        18.12        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       66.25        17.79        76.64        16.11        49.22        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       18.48        39.25        15.25        12.59        29.82         9.50 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       72.39        31.23        18.15        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      113.92        35.57        16.37        49.08        24.62        11.31 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       88.01        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       12.85         4.11        58.55       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        14.33        36.33        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-P6-A5OH 
       77.00        79.07        61.05        28.04        36.03         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        20.25        39.48        22.32 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            12.59              0.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           121.25            153.63 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            50.81             36.18 
[1] "12.6 - 121.2 (50.8)" "0.0 - 153.6 (36.2)" 
[1] "hr=" "2.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         1        8         1        4
  3P GAIN WILD-TYPE       8       35        17       14
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                8                35
  STAGE III               1                17
  STAGE IV                4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    1  9  2  2
  3P GAIN WILD-TYPE  8 39  9 18
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1                 8
  T2               9                39
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   13  1
  3P GAIN WILD-TYPE 65  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     13    1
  3P GAIN WILD-TYPE   65    9
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              13                65
  1               1                 9
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    9  5
  3P GAIN WILD-TYPE 50 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9    5
  3P GAIN WILD-TYPE   50   26
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               9                50
  MALE                 5                26
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   14  0
  3P GAIN WILD-TYPE 55 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     14    0
  3P GAIN WILD-TYPE   55   18
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               14                55
  YES               0                18
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  3P GAIN MUTATED                                       1
  3P GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  3P GAIN MUTATED                                          2
  3P GAIN WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  3P GAIN MUTATED                                     11
  3P GAIN WILD-TYPE                                   74
D5V8, multiclass
                                          clus
vv                                         3P GAIN MUTATED 3P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               2                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  11                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"
                   vv
clus                R0 R1 R2 RX
  3P GAIN MUTATED   11  0  2  0
  3P GAIN WILD-TYPE 52  7 10  5
D5V9, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              11                52
  R1               0                 7
  R2               2                10
  RX               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"
D5V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0    12
  3P GAIN WILD-TYPE     2                         1    64
D5V11, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  12                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"
D5V12, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  7
  3P GAIN WILD-TYPE  7 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    7
  3P GAIN WILD-TYPE    7   31
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               7                31
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   12  4
  3Q GAIN WILD-TYPE 45 29
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16                74 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                29 
$`3Q GAIN MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV 
       12.59        55.13        69.37        36.26       121.25        66.51 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5L2 TCGA-OR-A5L8 TCGA-OR-A5LJ 
       24.36        46.49        83.80        60.89        29.10        36.33 
TCGA-OR-A5LK TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       90.08        36.03        18.05        38.50 

$`3Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       44.45        30.31        18.12        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       66.25        17.79        76.64        16.11        49.22        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       18.48        39.25        15.25        12.59        29.82         9.50 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       72.39        31.23        18.15        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      113.92        35.57        16.37        49.08        24.62        11.31 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       88.01        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       12.85         4.11        58.55       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       52.24        78.41        14.33        53.03        61.08        77.00 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       79.07        61.05        28.04         0.00        24.85        20.25 
TCGA-PK-A5HA TCGA-PK-A5HC 
       39.48        22.32 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.59              0.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           121.25            153.63 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           42.495            37.410 
[1] "12.6 - 121.2 (42.5)" "0.0 - 153.6 (37.4)" 
[1] "hr=" "1.8"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         1        9         1        5
  3Q GAIN WILD-TYPE       8       34        17       13
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                9                34
  STAGE III               1                17
  STAGE IV                5                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    1 11  2  2
  3Q GAIN WILD-TYPE  8 37  9 18
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               1                 8
  T2              11                37
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   14  2
  3Q GAIN WILD-TYPE 64  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     14    2
  3Q GAIN WILD-TYPE   64    8
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              14                64
  1               2                 8
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   11  5
  3Q GAIN WILD-TYPE 48 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     11    5
  3Q GAIN WILD-TYPE   48   26
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              11                48
  MALE                 5                26
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   16  0
  3Q GAIN WILD-TYPE 53 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     16    0
  3Q GAIN WILD-TYPE   53   18
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               16                53
  YES               0                18
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  3Q GAIN MUTATED                                       1
  3Q GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  3Q GAIN MUTATED                                          2
  3Q GAIN WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  3Q GAIN MUTATED                                     13
  3Q GAIN WILD-TYPE                                   72
D6V8, multiclass
                                          clus
vv                                         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               2                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  13                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED   12  0  3  0
  3Q GAIN WILD-TYPE 51  7  9  5
D6V9, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              12                51
  R1               0                 7
  R2               3                 9
  RX               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"
D6V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0    13
  3Q GAIN WILD-TYPE     2                         1    63
D6V11, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  13                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"
D6V12, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    1  8
  3Q GAIN WILD-TYPE  7 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1    8
  3Q GAIN WILD-TYPE    7   30
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               8                30
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   26 12
  4P GAIN WILD-TYPE 31 21
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               38                52 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12                21 
$`4P GAIN MUTATED`
TCGA-OR-A5LB TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA 
       39.58        13.91        12.00        16.11        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       57.53        66.25        69.37        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5K3 
       67.59        36.26       121.25        29.82        66.51       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW 
       35.57        24.62        46.49        83.80       153.63        68.25 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5LA TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK 
       58.55        60.89        23.64        14.63        78.41        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT 
       53.03        61.08        77.00        79.07        36.03        18.05 
TCGA-OU-A5PI TCGA-PK-A5HC 
       38.50        22.32 

$`4P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD 
       55.13        68.75        88.87        19.04        18.12        99.88 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       69.21        17.79        18.48        39.25        15.25        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
        9.50        72.39        31.23        18.15        27.02       108.13 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ 
       32.68        16.37        49.08        11.31        24.36        88.01 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
       95.18       127.50        44.84        12.85         4.11       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        28.31        29.10        28.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LP TCGA-OR-A5LR 
       21.76        52.24        14.33        36.33        61.05        28.04 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
        0.00        24.85        20.25        39.48 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12                 0 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           153.63            152.15 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           51.125            31.510 
[1] "12.0 - 153.6 (51.1)" "0.0 - 152.2 (31.5)" 
[1] "hr=" "1.6"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         3       20         7        7
  4P GAIN WILD-TYPE       6       23        11       11
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 3                 6
  STAGE II               20                23
  STAGE III               7                11
  STAGE IV                7                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4P GAIN MUTATED    3 22  4  8
  4P GAIN WILD-TYPE  6 26  7 12
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               3                 6
  T2              22                26
  T3               4                 7
  T4               8                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   33  4
  4P GAIN WILD-TYPE 45  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     33    4
  4P GAIN WILD-TYPE   45    6
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              33                45
  1               4                 6
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   24 14
  4P GAIN WILD-TYPE 35 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     24   14
  4P GAIN WILD-TYPE   35   17
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              24                35
  MALE                14                17
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   31  6
  4P GAIN WILD-TYPE 38 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     31    6
  4P GAIN WILD-TYPE   38   12
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               31                38
  YES               6                12
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  4P GAIN MUTATED                                       1
  4P GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  4P GAIN MUTATED                                          3
  4P GAIN WILD-TYPE                                        1
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  4P GAIN MUTATED                                     34
  4P GAIN WILD-TYPE                                   51
D7V8, multiclass
                                          clus
vv                                         4P GAIN MUTATED 4P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               3                 1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  34                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  4P GAIN MUTATED   28  4  4  0
  4P GAIN WILD-TYPE 35  3  8  5
D7V9, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              28                35
  R1               4                 3
  R2               4                 8
  RX               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"
D7V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         0    30
  4P GAIN WILD-TYPE     1                         1    46
D7V11, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  30                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    4 13
  4P GAIN WILD-TYPE  4 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4   13
  4P GAIN WILD-TYPE    4   25
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              13                25
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   24 11
  4Q GAIN WILD-TYPE 33 22
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               35                55 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               11                22 
$`4Q GAIN MUTATED`
TCGA-OR-A5LB TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       39.58        13.91        12.00        44.45        30.31        57.53 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       66.25        69.37        76.64        16.11        49.22        67.59 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5K4 TCGA-OR-A5K8 
       36.26       121.25        29.82        66.51        35.57        24.62 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5LA 
       83.80       153.63        68.25         4.11        58.55        23.64 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       14.63        78.41        90.08        53.03        61.08        77.00 
TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5HC 
       79.07        36.03        18.05        38.50        22.32 

$`4Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       55.13        68.75        88.87        16.11        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       99.88        69.21        17.79        18.48        39.25        15.25 
TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
       12.59         9.50        72.39        31.23        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
      108.13        32.68       113.92        16.37        49.08        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       24.36        46.49        88.01        95.18       127.50        44.84 
TCGA-OR-A5KY TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 
       12.85        60.89       152.15        31.79        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI 
       28.64         5.23        39.35        21.76        52.24        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       36.33        61.05        28.04         0.00        24.85        20.25 
TCGA-PK-A5HA 
       39.48 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             4.11              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           153.63            152.15 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            49.22             32.68 
[1] "4.1 - 153.6 (49.2)" "0.0 - 152.2 (32.7)"
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         3       19         6        6
  4Q GAIN WILD-TYPE       6       24        12       12
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 3                 6
  STAGE II               19                24
  STAGE III               6                12
  STAGE IV                6                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4Q GAIN MUTATED    3 21  3  7
  4Q GAIN WILD-TYPE  6 27  8 13
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               3                 6
  T2              21                27
  T3               3                 8
  T4               7                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   30  4
  4Q GAIN WILD-TYPE 48  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     30    4
  4Q GAIN WILD-TYPE   48    6
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              30                48
  1               4                 6
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   21 14
  4Q GAIN WILD-TYPE 38 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     21   14
  4Q GAIN WILD-TYPE   38   17
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              21                38
  MALE                14                17
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   28  6
  4Q GAIN WILD-TYPE 41 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     28    6
  4Q GAIN WILD-TYPE   41   12
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               28                41
  YES               6                12
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  4Q GAIN MUTATED                                       1
  4Q GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  4Q GAIN MUTATED                                          2
  4Q GAIN WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  4Q GAIN MUTATED                                     32
  4Q GAIN WILD-TYPE                                   53
D8V8, multiclass
                                          clus
vv                                         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               2                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  32                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"
                   vv
clus                R0 R1 R2 RX
  4Q GAIN MUTATED   25  3  4  1
  4Q GAIN WILD-TYPE 38  4  8  4
D8V9, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              25                38
  R1               3                 4
  R2               4                 8
  RX               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"
D8V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         0    27
  4Q GAIN WILD-TYPE     1                         1    49
D8V11, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  27                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3 12
  4Q GAIN WILD-TYPE  5 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   12
  4Q GAIN WILD-TYPE    5   26
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              12                26
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   38 19
  5P GAIN WILD-TYPE 19 14
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               57                33 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19                14 
$`5P GAIN MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 
       43.30        39.58        12.59        68.75        13.91        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       88.87        16.11        19.04        44.45        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        67.59        36.26       121.25        29.82        66.51 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       18.15        27.02       108.13       113.92        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5L1 
       24.62        24.36        46.49        83.80       153.63        58.55 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       14.63        78.41        36.33        90.08        61.08        77.00 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       79.07        61.05        28.04        36.03        18.05        38.50 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5HC 
        0.00        24.85        22.32 

$`5P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5JB 
       33.83        91.30        42.51        44.55        55.13        18.12 
TCGA-OR-A5JD TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU 
       99.88        18.48        39.25        15.25        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KQ 
       72.39        31.23        32.68        49.08        11.31        88.01 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       95.18       127.50        68.25        44.84        12.85         4.11 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI 
       60.89       152.15        39.35        21.76        52.24        14.33 
TCGA-OR-A5LL TCGA-PK-A5H9 TCGA-PK-A5HA 
       53.03        20.25        39.48 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.00              4.11 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           153.63            152.15 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            36.26             39.48 
[1] "0.0 - 153.6 (36.3)" "4.1 - 152.2 (39.5)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         5       28        10       13
  5P GAIN WILD-TYPE       4       15         8        5
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 5                 4
  STAGE II               28                15
  STAGE III              10                 8
  STAGE IV               13                 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                T1 T2 T3 T4
  5P GAIN MUTATED    5 30  7 14
  5P GAIN WILD-TYPE  4 18  4  6
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               5                 4
  T2              30                18
  T3               7                 4
  T4              14                 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"
D9V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   50  6
  5P GAIN WILD-TYPE 28  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     50    6
  5P GAIN WILD-TYPE   28    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              50                28
  1               6                 4
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   37 20
  5P GAIN WILD-TYPE 22 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     37   20
  5P GAIN WILD-TYPE   22   11
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              37                22
  MALE                20                11
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   46  9
  5P GAIN WILD-TYPE 23  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     46    9
  5P GAIN WILD-TYPE   23    9
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               46                23
  YES               9                 9
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  5P GAIN MUTATED                                       1
  5P GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  5P GAIN MUTATED                                          3
  5P GAIN WILD-TYPE                                        1
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  5P GAIN MUTATED                                     53
  5P GAIN WILD-TYPE                                   32
D9V8, multiclass
                                          clus
vv                                         5P GAIN MUTATED 5P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               3                 1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  53                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   39  5  9  2
  5P GAIN WILD-TYPE 24  2  3  3
D9V9, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              39                24
  R1               5                 2
  R2               9                 3
  RX               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"
D9V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       1                         1    47
  5P GAIN WILD-TYPE     1                         0    29
D9V11, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  47                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    7 22
  5P GAIN WILD-TYPE  1 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   22
  5P GAIN WILD-TYPE    1   16
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              22                16
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   36 19
  5Q GAIN WILD-TYPE 21 14
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               55                35 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19                14 
$`5Q GAIN MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 
       43.30        39.58        12.59        68.75        13.91        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       88.87        16.11        19.04        44.45        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       67.59        36.26       121.25        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       31.23        18.15       108.13       113.92        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5L1 
       24.62        46.49        83.80       153.63        12.85        58.55 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       14.63        78.41        90.08        61.08        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG 
       24.85 

$`5Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5JB 
       33.83        91.30        42.51        44.55        55.13        18.12 
TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       99.88        49.22        18.48        39.25        15.25        12.59 
TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB 
        9.50        27.02        32.68        49.08        11.31        24.36 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       88.01        95.18       127.50        68.25        44.84         4.11 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI 
       60.89       152.15        39.35        21.76        52.24        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       36.33        53.03        20.25        39.48        22.32 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.00              4.11 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           153.63            152.15 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            36.26             39.35 
[1] "0.0 - 153.6 (36.3)" "4.1 - 152.2 (39.4)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         5       27        10       12
  5Q GAIN WILD-TYPE       4       16         8        6
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 5                 4
  STAGE II               27                16
  STAGE III              10                 8
  STAGE IV               12                 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"
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED    5 28  8 13
  5Q GAIN WILD-TYPE  4 20  3  7
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               5                 4
  T2              28                20
  T3               8                 3
  T4              13                 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"
D10V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   48  6
  5Q GAIN WILD-TYPE 30  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     48    6
  5Q GAIN WILD-TYPE   30    4
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              48                30
  1               6                 4
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   35 20
  5Q GAIN WILD-TYPE 24 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     35   20
  5Q GAIN WILD-TYPE   24   11
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              35                24
  MALE                20                11
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   44  9
  5Q GAIN WILD-TYPE 25  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     44    9
  5Q GAIN WILD-TYPE   25    9
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               44                25
  YES               9                 9
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  5Q GAIN MUTATED                                       1
  5Q GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  5Q GAIN MUTATED                                          3
  5Q GAIN WILD-TYPE                                        1
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  5Q GAIN MUTATED                                     51
  5Q GAIN WILD-TYPE                                   34
D10V8, multiclass
                                          clus
vv                                         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               3                 1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  51                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED   39  4  8  2
  5Q GAIN WILD-TYPE 24  3  4  3
D10V9, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              39                24
  R1               4                 3
  R2               8                 4
  RX               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"
D10V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         1    46
  5Q GAIN WILD-TYPE     2                         0    30
D10V11, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  46                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    7 20
  5Q GAIN WILD-TYPE  1 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   20
  5Q GAIN WILD-TYPE    1   18
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              20                18
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   10  8
  6P GAIN WILD-TYPE 47 25
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               18                72 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8                25 
$`6P GAIN MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC 
       13.91        88.87        16.11        19.04        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KT 
       69.21        67.59        18.48        24.36        46.49        95.18 
TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-PK-A5HC 
        4.11        31.79        90.08        61.08        77.00        22.32 

$`6P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JB 
       44.55        55.13        68.75        12.00        44.45        18.12 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       99.88        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       49.22        39.25        15.25        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU 
       49.08        24.62        11.31        88.01        83.80       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        44.84        12.85        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.35        21.76        14.63        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       36.33        53.03        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             4.11              0.00 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            95.18            153.63 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           39.140            38.875 
[1] "4.1 - 95.2 (39.1)"  "0.0 - 153.6 (38.9)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         3        6         4        4
  6P GAIN WILD-TYPE       6       37        14       14
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 3                 6
  STAGE II                6                37
  STAGE III               4                14
  STAGE IV                4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED    3  6  3  5
  6P GAIN WILD-TYPE  6 42  8 15
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               3                 6
  T2               6                42
  T3               3                 8
  T4               5                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   16  1
  6P GAIN WILD-TYPE 62  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16    1
  6P GAIN WILD-TYPE   62    9
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              16                62
  1               1                 9
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   13  5
  6P GAIN WILD-TYPE 46 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     13    5
  6P GAIN WILD-TYPE   46   26
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              13                46
  MALE                 5                26
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   15  2
  6P GAIN WILD-TYPE 54 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     15    2
  6P GAIN WILD-TYPE   54   16
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               15                54
  YES               2                16
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  6P GAIN MUTATED                                       0
  6P GAIN WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  6P GAIN MUTATED                                          1
  6P GAIN WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  6P GAIN MUTATED                                     17
  6P GAIN WILD-TYPE                                   68
D11V8, multiclass
                                          clus
vv                                         6P GAIN MUTATED 6P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  17                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"
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED   10  4  1  2
  6P GAIN WILD-TYPE 53  3 11  3
D11V9, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              10                53
  R1               4                 3
  R2               1                11
  RX               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"
D11V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         1    13
  6P GAIN WILD-TYPE     1                         0    63
D11V11, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  13                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"
D11V12, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    4  6
  6P GAIN WILD-TYPE  4 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    6
  6P GAIN WILD-TYPE    4   32
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO               6                32
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   10  6
  6Q GAIN WILD-TYPE 47 27
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                74 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6                27 
$`6Q GAIN MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JL 
       88.87        19.04        30.31        57.53        69.21        67.59 
TCGA-OR-A5KB TCGA-OR-A5KT TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5LE TCGA-OR-A5LK 
       24.36        95.18         4.11        31.79        21.76        90.08 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-PK-A5HA TCGA-PK-A5HC 
       61.08        77.00        39.48        22.32 

$`6Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        68.75        13.91        12.00        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       44.45        18.12        99.88        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       76.64        16.11        49.22        18.48        39.25        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       72.39        31.23        18.15        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      113.92        35.57        16.37        49.08        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        88.01        83.80       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L6 
       44.84        12.85        58.55        60.89       152.15        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF 
       29.10        28.64        23.64         5.23        39.35        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO 
       52.24        78.41        14.33        36.33        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 
       24.85        20.25 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             4.11              0.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            95.18            153.63 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           48.505            37.415 
[1] "4.1 - 95.2 (48.5)"  "0.0 - 153.6 (37.4)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         4        7         3        1
  6Q GAIN WILD-TYPE       5       36        15       17
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 4                 5
  STAGE II                7                36
  STAGE III               3                15
  STAGE IV                1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    4  7  1  3
  6Q GAIN WILD-TYPE  5 41 10 17
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               4                 5
  T2               7                41
  T3               1                10
  T4               3                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   15  0
  6Q GAIN WILD-TYPE 63 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15    0
  6Q GAIN WILD-TYPE   63   10
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              15                63
  1               0                10
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    9  7
  6Q GAIN WILD-TYPE 50 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      9    7
  6Q GAIN WILD-TYPE   50   24
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               9                50
  MALE                 7                24
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   14  1
  6Q GAIN WILD-TYPE 55 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     14    1
  6Q GAIN WILD-TYPE   55   17
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               14                55
  YES               1                17
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  6Q GAIN MUTATED                                       0
  6Q GAIN WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  6Q GAIN MUTATED                                          1
  6Q GAIN WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  6Q GAIN MUTATED                                     15
  6Q GAIN WILD-TYPE                                   70
D12V8, multiclass
                                          clus
vv                                         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  15                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"
                   vv
clus                R0 R1 R2 RX
  6Q GAIN MUTATED   11  2  0  2
  6Q GAIN WILD-TYPE 52  5 12  3
D12V9, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              11                52
  R1               2                 5
  R2               0                12
  RX               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"
D12V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       1                         1    10
  6Q GAIN WILD-TYPE     1                         0    66
D12V11, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  10                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    2  6
  6Q GAIN WILD-TYPE  6 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    6
  6Q GAIN WILD-TYPE    6   32
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               6                32
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   30 18
  7P GAIN WILD-TYPE 27 15
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               48                42 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18                15 
$`7P GAIN MUTATED`
TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       39.58        55.13        68.75        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ 
       19.04        30.31        66.25        17.79        69.37        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        67.59        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K8 
       31.23        18.15       108.13       113.92        16.37        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY 
       24.36        46.49        83.80       153.63        68.25        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LA 
        4.11        58.55        60.89        31.79        29.10        23.64 
TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
        5.23        14.63        78.41        36.33        90.08        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PA-A5YG 
       77.00        79.07        61.05        36.03        38.50        24.85 

$`7P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        12.59        42.51        44.55 
TCGA-OR-A5J4 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       13.91        44.45        18.12        57.53        99.88        69.21 
TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU 
       76.64        18.48        39.25        15.25        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JZ TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 
       72.39        27.02        32.68        35.57        49.08        11.31 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L6 
       88.01        95.18       127.50        44.84       152.15        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL 
       28.64        39.35        21.76        52.24        14.33        53.03 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       28.04        18.05         0.00        20.25        39.48        22.32 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             4.11              0.00 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           153.63            152.15 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            39.04             37.41 
[1] "4.1 - 153.6 (39.0)" "0.0 - 152.2 (37.4)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         2       25         9       12
  7P GAIN WILD-TYPE       7       18         9        6
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 2                 7
  STAGE II               25                18
  STAGE III               9                 9
  STAGE IV               12                 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"
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    2 28  7 11
  7P GAIN WILD-TYPE  7 20  4  9
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               2                 7
  T2              28                20
  T3               7                 4
  T4              11                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   41  7
  7P GAIN WILD-TYPE 37  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     41    7
  7P GAIN WILD-TYPE   37    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              41                37
  1               7                 3
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   31 17
  7P GAIN WILD-TYPE 28 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     31   17
  7P GAIN WILD-TYPE   28   14
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              31                28
  MALE                17                14
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   38  9
  7P GAIN WILD-TYPE 31  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     38    9
  7P GAIN WILD-TYPE   31    9
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               38                31
  YES               9                 9
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  7P GAIN MUTATED                                       1
  7P GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  7P GAIN MUTATED                                          3
  7P GAIN WILD-TYPE                                        1
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  7P GAIN MUTATED                                     44
  7P GAIN WILD-TYPE                                   41
D13V8, multiclass
                                          clus
vv                                         7P GAIN MUTATED 7P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               3                 1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  44                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   33  3  8  3
  7P GAIN WILD-TYPE 30  4  4  2
D13V9, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              33                30
  R1               3                 4
  R2               8                 4
  RX               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"
D13V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       0                         1    41
  7P GAIN WILD-TYPE     2                         0    35
D13V11, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  41                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    6 20
  7P GAIN WILD-TYPE  2 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6   20
  7P GAIN WILD-TYPE    2   18
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO              20                18
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   31 17
  7Q GAIN WILD-TYPE 26 16
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48                42 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               17                16 
$`7Q GAIN MUTATED`
TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       39.58        55.13        68.75        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       19.04        44.45        30.31        66.25        17.79        69.37 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       16.11        49.22        67.59        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K8 
       66.51        31.23        18.15       108.13       113.92        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY 
       24.36        46.49        83.80       153.63        68.25        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LA 
        4.11        58.55        60.89        31.79        29.10        23.64 
TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
        5.23        14.63        78.41        36.33        90.08        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PA-A5YG 
       77.00        79.07        61.05        36.03        38.50        24.85 

$`7Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        12.59        42.51        44.55 
TCGA-OR-A5J4 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JI 
       13.91        18.12        57.53        99.88        69.21        76.64 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW 
       18.48        39.25        15.25        12.59         9.50        72.39 
TCGA-OR-A5JZ TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       27.02        32.68        35.57        16.37        49.08        11.31 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L6 
       88.01        95.18       127.50        44.84       152.15        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL 
       28.64        39.35        21.76        52.24        14.33        53.03 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       28.04        18.05         0.00        20.25        39.48        22.32 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             4.11              0.00 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           153.63            152.15 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           42.015            34.700 
[1] "4.1 - 153.6 (42.0)" "0.0 - 152.2 (34.7)"
[1] "hr=" "1.3"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         2       26         8       12
  7Q GAIN WILD-TYPE       7       17        10        6
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 2                 7
  STAGE II               26                17
  STAGE III               8                10
  STAGE IV               12                 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"
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    2 29  6 11
  7Q GAIN WILD-TYPE  7 19  5  9
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               2                 7
  T2              29                19
  T3               6                 5
  T4              11                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   41  7
  7Q GAIN WILD-TYPE 37  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     41    7
  7Q GAIN WILD-TYPE   37    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              41                37
  1               7                 3
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   31 17
  7Q GAIN WILD-TYPE 28 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     31   17
  7Q GAIN WILD-TYPE   28   14
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              31                28
  MALE                17                14
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   39  8
  7Q GAIN WILD-TYPE 30 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     39    8
  7Q GAIN WILD-TYPE   30   10
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               39                30
  YES               8                10
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  7Q GAIN MUTATED                                       1
  7Q GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  7Q GAIN MUTATED                                          3
  7Q GAIN WILD-TYPE                                        1
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  7Q GAIN MUTATED                                     44
  7Q GAIN WILD-TYPE                                   41
D14V8, multiclass
                                          clus
vv                                         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               3                 1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  44                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   33  3  8  3
  7Q GAIN WILD-TYPE 30  4  4  2
D14V9, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              33                30
  R1               3                 4
  R2               8                 4
  RX               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"
D14V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       0                         1    41
  7Q GAIN WILD-TYPE     2                         0    35
D14V11, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  41                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7 20
  7Q GAIN WILD-TYPE  1 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7   20
  7Q GAIN WILD-TYPE    1   18
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              20                18
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   24  8
  8P GAIN WILD-TYPE 33 25
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32                58 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8                25 
$`8P GAIN MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J9 TCGA-OR-A5JC 
       43.30        13.91        12.00        88.87        44.45        57.53 
TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       69.37        49.22        18.48        15.25        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K4 
       29.82        66.51        31.23        27.02       108.13        35.57 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KZ 
       11.31        46.49        83.80       153.63        68.25         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF 
       58.55        29.10        28.64        23.64         5.23        14.63 
TCGA-OR-A5LN TCGA-OR-A5LR 
       77.00        28.04 

$`8P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       55.13        68.75        16.11        19.04        30.31        18.12 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ 
       99.88        69.21        66.25        17.79        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY 
       67.59        39.25        12.59         9.50        72.39        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB 
       32.68       113.92        16.37        49.08        24.62        24.36 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L2 
       88.01        95.18       127.50        44.84        12.85        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
      152.15        31.79        28.31        39.35        21.76        52.24 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       78.41        14.33        36.33        90.08        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       79.07        61.05        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        20.25        39.48        22.32 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             4.11              0.00 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           153.63            152.15 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           35.915            39.300 
[1] "4.1 - 153.6 (35.9)" "0.0 - 152.2 (39.3)"
[1] "hr=" "1.6"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         2       19         5        5
  8P GAIN WILD-TYPE       7       24        13       13
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 2                 7
  STAGE II               19                24
  STAGE III               5                13
  STAGE IV                5                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    2 20  3  6
  8P GAIN WILD-TYPE  7 28  8 14
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               2                 7
  T2              20                28
  T3               3                 8
  T4               6                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   29  2
  8P GAIN WILD-TYPE 49  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     29    2
  8P GAIN WILD-TYPE   49    8
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              29                49
  1               2                 8
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   21 11
  8P GAIN WILD-TYPE 38 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     21   11
  8P GAIN WILD-TYPE   38   20
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              21                38
  MALE                11                20
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   24  7
  8P GAIN WILD-TYPE 45 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     24    7
  8P GAIN WILD-TYPE   45   11
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               24                45
  YES               7                11
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  8P GAIN MUTATED                                       1
  8P GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  8P GAIN MUTATED                                          1
  8P GAIN WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  8P GAIN MUTATED                                     30
  8P GAIN WILD-TYPE                                   55
D15V8, multiclass
                                          clus
vv                                         8P GAIN MUTATED 8P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  30                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"
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED   23  2  4  2
  8P GAIN WILD-TYPE 40  5  8  3
D15V9, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              23                40
  R1               2                 5
  R2               4                 8
  RX               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"
D15V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         1    29
  8P GAIN WILD-TYPE     2                         0    47
D15V11, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  29                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4 12
  8P GAIN WILD-TYPE  4 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4   12
  8P GAIN WILD-TYPE    4   26
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              12                26
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   26 12
  8Q GAIN WILD-TYPE 31 21
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               38                52 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12                21 
$`8Q GAIN MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J9 TCGA-OR-A5JC 
       43.30        13.91        12.00        88.87        44.45        57.53 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP 
       66.25        69.37        16.11        49.22        18.48        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ 
       36.26       121.25        29.82        66.51        31.23        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
      108.13        35.57        16.37        11.31        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       83.80       153.63        68.25         4.11        58.55        60.89 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF 
       29.10        28.64        23.64         5.23        39.35        14.63 
TCGA-OR-A5LN TCGA-OR-A5LR 
       77.00        28.04 

$`8Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       55.13        68.75        16.11        19.04        30.31        18.12 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JO 
       99.88        69.21        17.79        76.64        67.59        39.25 
TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K3 
       12.59         9.50        72.39        18.15        32.68       113.92 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       49.08        24.62        88.01        95.18       127.50        44.84 
TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LE TCGA-OR-A5LG 
       12.85       152.15        31.79        28.31        21.76        52.24 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       78.41        14.33        36.33        90.08        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       79.07        61.05        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        20.25        39.48        22.32 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             4.11              0.00 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           153.63            152.15 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           35.915            39.365 
[1] "4.1 - 153.6 (35.9)" "0.0 - 152.2 (39.4)"
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         2       22         7        6
  8Q GAIN WILD-TYPE       7       21        11       12
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 2                 7
  STAGE II               22                21
  STAGE III               7                11
  STAGE IV                6                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED    2 23  4  8
  8Q GAIN WILD-TYPE  7 25  7 12
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               2                 7
  T2              23                25
  T3               4                 7
  T4               8                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   34  3
  8Q GAIN WILD-TYPE 44  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     34    3
  8Q GAIN WILD-TYPE   44    7
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              34                44
  1               3                 7
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   25 13
  8Q GAIN WILD-TYPE 34 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     25   13
  8Q GAIN WILD-TYPE   34   18
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              25                34
  MALE                13                18
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   28  9
  8Q GAIN WILD-TYPE 41  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     28    9
  8Q GAIN WILD-TYPE   41    9
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               28                41
  YES               9                 9
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  8Q GAIN MUTATED                                       1
  8Q GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  8Q GAIN MUTATED                                          1
  8Q GAIN WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  8Q GAIN MUTATED                                     36
  8Q GAIN WILD-TYPE                                   49
D16V8, multiclass
                                          clus
vv                                         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  36                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   27  2  5  3
  8Q GAIN WILD-TYPE 36  5  7  2
D16V9, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              27                36
  R1               2                 5
  R2               5                 7
  RX               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"
D16V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       0                         1    35
  8Q GAIN WILD-TYPE     2                         0    41
D16V11, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  35                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    4 15
  8Q GAIN WILD-TYPE  4 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4   15
  8Q GAIN WILD-TYPE    4   23
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              15                23
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED   11 10
  9P GAIN WILD-TYPE 46 23
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               21                69 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10                23 
$`9P GAIN MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JF 
       91.30        13.91        12.00        16.11        30.31        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JQ TCGA-OR-A5K8 TCGA-OR-A5KO 
       17.79        69.37        16.11        36.26        24.62        46.49 
TCGA-OR-A5KS TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5LJ TCGA-OR-A5LL 
       83.80        12.85         4.11        58.55        36.33        53.03 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       36.03        18.05        38.50 

$`9P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        43.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB 
       55.13        68.75        88.87        19.04        44.45        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL 
       57.53        99.88        69.21        76.64        49.22        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       18.48        39.25        15.25       121.25        12.59        29.82 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
        9.50        66.51        72.39        31.23        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
      108.13        32.68       113.92        35.57        16.37        49.08 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       11.31        24.36        88.01        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       68.25        44.84        60.89       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LM 
       14.63        52.24        78.41        14.33        90.08        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OH TCGA-PA-A5YG 
       77.00        79.07        61.05        28.04         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       20.25        39.48        22.32 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             4.11              0.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            91.30            153.63 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            36.03             39.58 
[1] "4.1 - 91.3 (36.0)"  "0.0 - 153.6 (39.6)"
[1] "hr=" "1.8"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         0       10         3        8
  9P GAIN WILD-TYPE       9       33        15       10
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0                 9
  STAGE II               10                33
  STAGE III               3                15
  STAGE IV                8                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    0 12  3  6
  9P GAIN WILD-TYPE  9 36  8 14
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               0                 9
  T2              12                36
  T3               3                 8
  T4               6                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   15  6
  9P GAIN WILD-TYPE 63  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15    6
  9P GAIN WILD-TYPE   63    4
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              15                63
  1               6                 4
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   14  7
  9P GAIN WILD-TYPE 45 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     14    7
  9P GAIN WILD-TYPE   45   24
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              14                45
  MALE                 7                24
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   19  1
  9P GAIN WILD-TYPE 50 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     19    1
  9P GAIN WILD-TYPE   50   17
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               19                50
  YES               1                17
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  9P GAIN MUTATED                                       1
  9P GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  9P GAIN MUTATED                                          1
  9P GAIN WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  9P GAIN MUTATED                                     19
  9P GAIN WILD-TYPE                                   66
D17V8, multiclass
                                          clus
vv                                         9P GAIN MUTATED 9P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  19                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  9P GAIN MUTATED   11  3  5  1
  9P GAIN WILD-TYPE 52  4  7  4
D17V9, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              11                52
  R1               3                 4
  R2               5                 7
  RX               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"
D17V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         0    18
  9P GAIN WILD-TYPE     2                         1    58
D17V11, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  18                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  9
  9P GAIN WILD-TYPE  5 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    9
  9P GAIN WILD-TYPE    5   29
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO               9                29
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   12 15
  9Q GAIN WILD-TYPE 45 18
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               27                63 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               15                18 
$`9Q GAIN MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5JA 
       91.30        39.58        13.91        12.00        16.11        30.31 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JQ 
       69.21        66.25        17.79        69.37        16.11        36.26 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KY 
       18.15        32.68        24.62        46.49        83.80        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT 
        4.11        58.55        36.33        53.03        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5HC 
       38.50         0.00        22.32 

$`9Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        43.30        12.59        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC 
       68.75        88.87        19.04        44.45        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       99.88        76.64        49.22        67.59        18.48        39.25 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       15.25       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       72.39        31.23        27.02       108.13       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT 
       16.37        49.08        11.31        24.36        88.01        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 
      153.63       127.50        68.25        44.84        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.35        21.76        14.63        52.24        78.41        14.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        61.08        77.00        79.07        61.05        28.04 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       24.85        20.25        39.48 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.00              5.23 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            91.30            153.63 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            32.68             43.30 
[1] "0.0 - 91.3 (32.7)"  "5.2 - 153.6 (43.3)"
[1] "hr=" "2.6"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         1       10         5       11
  9Q GAIN WILD-TYPE       8       33        13        7
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II               10                33
  STAGE III               5                13
  STAGE IV               11                 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"
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    1 12  3 11
  9Q GAIN WILD-TYPE  8 36  8  9
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               1                 8
  T2              12                36
  T3               3                 8
  T4              11                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   20  7
  9Q GAIN WILD-TYPE 58  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     20    7
  9Q GAIN WILD-TYPE   58    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              20                58
  1               7                 3
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   19  8
  9Q GAIN WILD-TYPE 40 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19    8
  9Q GAIN WILD-TYPE   40   23
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              19                40
  MALE                 8                23
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   22  4
  9Q GAIN WILD-TYPE 47 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     22    4
  9Q GAIN WILD-TYPE   47   14
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               22                47
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  9Q GAIN MUTATED                                       1
  9Q GAIN WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  9Q GAIN MUTATED                                          1
  9Q GAIN WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  9Q GAIN MUTATED                                     25
  9Q GAIN WILD-TYPE                                   60
D18V8, multiclass
                                          clus
vv                                         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  25                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"
                   vv
clus                R0 R1 R2 RX
  9Q GAIN MUTATED   14  4  7  1
  9Q GAIN WILD-TYPE 49  3  5  4
D18V9, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              14                49
  R1               4                 3
  R2               7                 5
  RX               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"
D18V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       1                         0    23
  9Q GAIN WILD-TYPE     1                         1    53
D18V11, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  23                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"
D18V12, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    3 12
  9Q GAIN WILD-TYPE  5 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3   12
  9Q GAIN WILD-TYPE    5   26
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              12                26
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   12 13
  10P GAIN WILD-TYPE 45 20
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                25                 65 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                 20 
$`10P GAIN MUTATED`
TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 
       39.58        12.59        55.13        12.00        16.11        44.45 
TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JX TCGA-OR-A5K2 
       57.53        66.25        49.22        15.25        31.23        32.68 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KY TCGA-OR-A5L8 TCGA-OR-A5LC 
       24.62        24.36        46.49        12.85        29.10         5.23 
TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT 
       39.35        14.33        36.33        79.07        36.03        18.05 
TCGA-OU-A5PI 
       38.50 

$`10P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       33.83        91.30        43.30        42.51        44.55        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       13.91        88.87        19.04        30.31        18.12        99.88 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL 
       69.21        17.79        69.37        76.64        16.11        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       18.48        39.25        36.26       121.25        12.59        29.82 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
        9.50        66.51        72.39        18.15        27.02       108.13 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KQ 
      113.92        35.57        16.37        49.08        11.31        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       28.64        23.64        21.76        14.63        52.24        78.41 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        53.03        61.08        77.00        61.05        28.04 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
        0.00        24.85        20.25        39.48        22.32 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              5.23               0.00 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             79.07             153.63 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             32.68              43.30 
[1] "5.2 - 79.1 (32.7)"  "0.0 - 153.6 (43.3)"
[1] "hr=" "2.5"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         0        8         6       10
  10P GAIN WILD-TYPE       9       35        12        8
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 8                 35
  STAGE III                6                 12
  STAGE IV                10                  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"
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    0 10  4 10
  10P GAIN WILD-TYPE  9 38  7 10
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  9
  T2               10                 38
  T3                4                  7
  T4               10                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   21  3
  10P GAIN WILD-TYPE 57  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     21    3
  10P GAIN WILD-TYPE   57    7
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               21                 57
  1                3                  7
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   16  9
  10P GAIN WILD-TYPE 43 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     16    9
  10P GAIN WILD-TYPE   43   22
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               16                 43
  MALE                  9                 22
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   19  5
  10P GAIN WILD-TYPE 50 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     19    5
  10P GAIN WILD-TYPE   50   13
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                19                 50
  YES                5                 13
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  10P GAIN MUTATED                                       0
  10P GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  10P GAIN MUTATED                                          0
  10P GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  10P GAIN MUTATED                                     25
  10P GAIN WILD-TYPE                                   60
D19V8, multiclass
                                          clus
vv                                         10P GAIN MUTATED 10P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   25                 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"
                    vv
clus                 R0 R1 R2 RX
  10P GAIN MUTATED   13  1  8  1
  10P GAIN WILD-TYPE 50  6  4  4
D19V9, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               13                 50
  R1                1                  6
  R2                8                  4
  RX                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"
D19V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0    22
  10P GAIN WILD-TYPE     2                         1    54
D19V11, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   22                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4 12
  10P GAIN WILD-TYPE  4 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4   12
  10P GAIN WILD-TYPE    4   26
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               12                 26
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED   11 15
  10Q GAIN WILD-TYPE 46 18
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                 64 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                15                 18 
$`10Q GAIN MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5J7 
       91.30        39.58        12.59        55.13        12.00        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP 
       44.45        57.53        66.25        49.22        18.48        15.25 
TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K8 TCGA-OR-A5KY TCGA-OR-A5L8 TCGA-OR-A5LC 
       31.23        32.68        24.62        12.85        29.10         5.23 
TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT 
       39.35        14.33        36.33        79.07        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH 
       38.50         0.00 

$`10Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 
       33.83        43.30        42.51        44.55        68.75        13.91 
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE 
       88.87        19.04        30.31        18.12        99.88        69.21 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO 
       17.79        69.37        76.64        16.11        67.59        39.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       72.39        18.15        27.02       108.13       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       16.37        49.08        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       28.64        23.64        21.76        14.63        52.24        78.41 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        53.03        61.08        77.00        61.05        28.04 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        20.25        39.48        22.32 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.00               4.11 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             91.30             153.63 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            31.955             43.925 
[1] "0.0 - 91.3 (32.0)"  "4.1 - 153.6 (43.9)"
[1] "hr=" "3"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         0        8         6       11
  10Q GAIN WILD-TYPE       9       35        12        7
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 8                 35
  STAGE III                6                 12
  STAGE IV                11                  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"
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN MUTATED    0 10  4 11
  10Q GAIN WILD-TYPE  9 38  7  9
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  9
  T2               10                 38
  T3                4                  7
  T4               11                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   22  3
  10Q GAIN WILD-TYPE 56  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     22    3
  10Q GAIN WILD-TYPE   56    7
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               22                 56
  1                3                  7
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   17  9
  10Q GAIN WILD-TYPE 42 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     17    9
  10Q GAIN WILD-TYPE   42   22
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               17                 42
  MALE                  9                 22
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   19  6
  10Q GAIN WILD-TYPE 50 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     19    6
  10Q GAIN WILD-TYPE   50   12
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                19                 50
  YES                6                 12
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  10Q GAIN MUTATED                                       0
  10Q GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  10Q GAIN MUTATED                                          0
  10Q GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  10Q GAIN MUTATED                                     26
  10Q GAIN WILD-TYPE                                   59
D20V8, multiclass
                                          clus
vv                                         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   26                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  10Q GAIN MUTATED   12  2  9  1
  10Q GAIN WILD-TYPE 51  5  3  4
D20V9, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               12                 51
  R1                2                  5
  R2                9                  3
  RX                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"
D20V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0    23
  10Q GAIN WILD-TYPE     2                         1    53
D20V11, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   23                 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"
D20V12, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    4 12
  10Q GAIN WILD-TYPE  4 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4   12
  10Q GAIN WILD-TYPE    4   26
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               12                 26
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    0  5
  11P GAIN WILD-TYPE 57 28
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 85 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 28 
$`11P GAIN MUTATED`
TCGA-P6-A5OG TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-P6-A5OH 
       12.59        60.89        39.35        14.33         0.00 

$`11P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        30.31        18.12        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        67.59        18.48        39.25        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       35.57        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
       68.25        44.84        12.85         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        52.24        78.41        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       36.03        18.05        38.50        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.00               4.11 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             60.89             153.63 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             14.33              39.25 
[1] "0.0 - 60.9 (14.3)"  "4.1 - 153.6 (39.2)"
[1] "hr=" "5.5"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         0        1         1        3
  11P GAIN WILD-TYPE       9       42        17       15
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                1                 17
  STAGE IV                 3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    0  1  0  4
  11P GAIN WILD-TYPE  9 47 11 16
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                0                 11
  T4                4                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    5  0
  11P GAIN WILD-TYPE 73 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    0
  11P GAIN WILD-TYPE   73   10
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                5                 73
  1                0                 10
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  1
  11P GAIN WILD-TYPE 55 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    1
  11P GAIN WILD-TYPE   55   30
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                4                 55
  MALE                  1                 30
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    5  0
  11P GAIN WILD-TYPE 64 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    0
  11P GAIN WILD-TYPE   64   18
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 5                 64
  YES                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  11P GAIN MUTATED                                       0
  11P GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  11P GAIN MUTATED                                          0
  11P GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  11P GAIN MUTATED                                      5
  11P GAIN WILD-TYPE                                   80
D21V8, multiclass
                                          clus
vv                                         11P GAIN MUTATED 11P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    5                 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"
                    vv
clus                 R0 R1 R2 RX
  11P GAIN MUTATED    1  0  3  1
  11P GAIN WILD-TYPE 62  7  9  4
D21V9, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                1                 62
  R1                0                  7
  R2                3                  9
  RX                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"
D21V10, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 30 
        TCGA-OR-A5KP         TCGA-OR-A5J2         TCGA-OR-A5J3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J7         TCGA-OR-A5J8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-OR-A5JG         TCGA-OR-A5JJ         TCGA-OR-A5JT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JX         TCGA-OR-A5JY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K5         TCGA-OR-A5KB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-OR-A5KY         TCGA-OR-A5L9         TCGA-OR-A5LG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LM         TCGA-OR-A5LN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-OR-A5LO         TCGA-OR-A5LP         TCGA-OR-A5LT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-OU-A5PI         TCGA-PK-A5HA         TCGA-PK-A5HC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0     5
  11P GAIN WILD-TYPE     2                         1    71
D21V11, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    0  5
  11P GAIN WILD-TYPE  8 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    5
  11P GAIN WILD-TYPE    8   33
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                5                 33
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    0  6
  11Q GAIN WILD-TYPE 57 27
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 84 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 27 
$`11Q GAIN MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J7 TCGA-OR-A5K5 TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LI 
       12.59        16.11        16.37        60.89        39.35        14.33 

$`11Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       55.13        68.75        13.91        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       44.45        30.31        18.12        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       66.25        17.79        69.37        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       67.59        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.08        24.62        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       12.85         4.11        58.55       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF 
       29.10        28.64        23.64         5.23        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        36.33        90.08        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       77.00        79.07        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50         0.00        24.85        20.25        39.48        22.32 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             12.59               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             60.89             153.63 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            16.240             39.365 
[1] "12.6 - 60.9 (16.2)" "0.0 - 153.6 (39.4)"
[1] "hr=" "5.3"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         0        1         3        2
  11Q GAIN WILD-TYPE       9       42        15       16
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                3                 15
  STAGE IV                 2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    0  1  2  3
  11Q GAIN WILD-TYPE  9 47  9 17
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                2                  9
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    6  0
  11Q GAIN WILD-TYPE 72 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    0
  11Q GAIN WILD-TYPE   72   10
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                6                 72
  1                0                 10
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  1
  11Q GAIN WILD-TYPE 54 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    1
  11Q GAIN WILD-TYPE   54   30
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                5                 54
  MALE                  1                 30
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  1
  11Q GAIN WILD-TYPE 64 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    1
  11Q GAIN WILD-TYPE   64   17
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 5                 64
  YES                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  11Q GAIN MUTATED                                       0
  11Q GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  11Q GAIN MUTATED                                          0
  11Q GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  11Q GAIN MUTATED                                      6
  11Q GAIN WILD-TYPE                                   79
D22V8, multiclass
                                          clus
vv                                         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    6                 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"
                    vv
clus                 R0 R1 R2 RX
  11Q GAIN MUTATED    2  1  2  1
  11Q GAIN WILD-TYPE 61  6 10  4
D22V9, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                2                 61
  R1                1                  6
  R2                2                 10
  RX                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"
D22V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0     6
  11Q GAIN WILD-TYPE     2                         1    70
D22V11, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    6                 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"
D22V12, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1  4
  11Q GAIN WILD-TYPE  7 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    4
  11Q GAIN WILD-TYPE    7   34
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                4                 34
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   40 24
  12P GAIN WILD-TYPE 17  9
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                64                 26 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                24                  9 
$`12P GAIN MUTATED`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        43.30        39.58        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA 
       12.00        88.87        16.11        19.04        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       57.53        69.21        66.25        17.79        69.37        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ 
       16.11        49.22        67.59        18.48        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        29.82        66.51        31.23        27.02       108.13 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KS TCGA-OR-A5KU 
       32.68       113.92        35.57        24.62        83.80       153.63 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 
       68.25        12.85         4.11        58.55        60.89        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        29.10        28.64        23.64         5.23        39.35 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
       14.63        78.41        14.33        36.33        90.08        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       77.00        79.07        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5HC 
       38.50         0.00        24.85        22.32 

$`12P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JD 
       33.83        12.59        42.51        44.55        18.12        99.88 
TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K5 
       39.25        12.59         9.50        72.39        18.15        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT 
       49.08        11.31        24.36        46.49        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL 
      127.50        44.84       152.15        21.76        52.24        53.03 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               0.0                9.5 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            153.63             152.15 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            36.295             40.995 
[1] "0.0 - 153.6 (36.3)" "9.5 - 152.2 (41.0)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         5       31        13       14
  12P GAIN WILD-TYPE       4       12         5        4
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  5                  4
  STAGE II                31                 12
  STAGE III               13                  5
  STAGE IV                14                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    5 34  8 16
  12P GAIN WILD-TYPE  4 14  3  4
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                5                  4
  T2               34                 14
  T3                8                  3
  T4               16                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   56  7
  12P GAIN WILD-TYPE 22  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     56    7
  12P GAIN WILD-TYPE   22    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               56                 22
  1                7                  3
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   40 24
  12P GAIN WILD-TYPE 19  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     40   24
  12P GAIN WILD-TYPE   19    7
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               40                 19
  MALE                 24                  7
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   51 11
  12P GAIN WILD-TYPE 18  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     51   11
  12P GAIN WILD-TYPE   18    7
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                51                 18
  YES               11                  7
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  12P GAIN MUTATED                                       1
  12P GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  12P GAIN MUTATED                                          3
  12P GAIN WILD-TYPE                                        1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  12P GAIN MUTATED                                     60
  12P GAIN WILD-TYPE                                   25
D23V8, multiclass
                                          clus
vv                                         12P GAIN MUTATED 12P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                3                  1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   60                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED   42  6 10  4
  12P GAIN WILD-TYPE 21  1  2  1
D23V9, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               42                 21
  R1                6                  1
  R2               10                  2
  RX                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"
D23V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       1                         1    54
  12P GAIN WILD-TYPE     1                         0    22
D23V11, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   54                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    8 26
  12P GAIN WILD-TYPE  0 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8   26
  12P GAIN WILD-TYPE    0   12
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                  0
  NOT HISPANIC OR LATINO               26                 12
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   40 24
  12Q GAIN WILD-TYPE 17  9
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                64                 26 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                24                  9 
$`12Q GAIN MUTATED`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        43.30        39.58        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA 
       12.00        88.87        16.11        19.04        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       57.53        69.21        66.25        17.79        69.37        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       16.11        49.22        67.59        15.25        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       29.82        66.51        31.23        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KS TCGA-OR-A5KU 
      113.92        35.57        16.37        24.62        83.80       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       68.25        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        14.63        78.41        14.33        36.33        90.08 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG 
       18.05        38.50         0.00        24.85 

$`12Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JD 
       33.83        12.59        42.51        44.55        18.12        99.88 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY 
       18.48        39.25        12.59         9.50        72.39        18.15 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT 
       49.08        11.31        24.36        46.49        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL TCGA-PK-A5H9 
      127.50       152.15        21.76        52.24        53.03        20.25 
TCGA-PK-A5HA TCGA-PK-A5HC 
       39.48        22.32 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               0.0                9.5 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            153.63             152.15 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            37.415             39.365 
[1] "0.0 - 153.6 (37.4)" "9.5 - 152.2 (39.4)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         5       31        14       13
  12Q GAIN WILD-TYPE       4       12         4        5
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  5                  4
  STAGE II                31                 12
  STAGE III               14                  4
  STAGE IV                13                  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                 T1 T2 T3 T4
  12Q GAIN MUTATED    5 35  9 14
  12Q GAIN WILD-TYPE  4 13  2  6
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                5                  4
  T2               35                 13
  T3                9                  2
  T4               14                  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"
D24V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   55  8
  12Q GAIN WILD-TYPE 23  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     55    8
  12Q GAIN WILD-TYPE   23    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               55                 23
  1                8                  2
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   40 24
  12Q GAIN WILD-TYPE 19  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     40   24
  12Q GAIN WILD-TYPE   19    7
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               40                 19
  MALE                 24                  7
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   51 11
  12Q GAIN WILD-TYPE 18  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     51   11
  12Q GAIN WILD-TYPE   18    7
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                51                 18
  YES               11                  7
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  12Q GAIN MUTATED                                       1
  12Q GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  12Q GAIN MUTATED                                          3
  12Q GAIN WILD-TYPE                                        1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  12Q GAIN MUTATED                                     60
  12Q GAIN WILD-TYPE                                   25
D24V8, multiclass
                                          clus
vv                                         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                3                  1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   60                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN MUTATED   44  4 10  4
  12Q GAIN WILD-TYPE 19  3  2  1
D24V9, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               44                 19
  R1                4                  3
  R2               10                  2
  RX                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"
D24V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       0                         1    55
  12Q GAIN WILD-TYPE     2                         0    21
D24V11, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   55                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8 26
  12Q GAIN WILD-TYPE  0 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8   26
  12Q GAIN WILD-TYPE    0   12
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                  0
  NOT HISPANIC OR LATINO               26                 12
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    4  2
  13Q GAIN WILD-TYPE 53 31
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 84 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 31 
$`13Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JL TCGA-OR-A5K8 TCGA-OR-A5KW TCGA-OR-A5LC TCGA-OR-A5LM 
       55.13        67.59        24.62        68.25         5.23        61.08 

$`13Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        30.31        18.12        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       49.22        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       16.37        49.08        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY 
       83.80        95.18       153.63       127.50        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       29.10        28.64        23.64        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        36.33        90.08        53.03 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       77.00        79.07        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50         0.00        24.85        20.25        39.48        22.32 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              5.23               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             68.25             153.63 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            58.105             37.415 
[1] "5.2 - 68.2 (58.1)"  "0.0 - 153.6 (37.4)"
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         1        2         1        2
  13Q GAIN WILD-TYPE       8       41        17       16
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 2                 41
  STAGE III                1                 17
  STAGE IV                 2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    1  3  1  1
  13Q GAIN WILD-TYPE  8 45 10 19
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                1                  8
  T2                3                 45
  T3                1                 10
  T4                1                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5  1
  13Q GAIN WILD-TYPE 73  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    1
  13Q GAIN WILD-TYPE   73    9
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                5                 73
  1                1                  9
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  2
  13Q GAIN WILD-TYPE 55 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    2
  13Q GAIN WILD-TYPE   55   29
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                 55
  MALE                  2                 29
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5  1
  13Q GAIN WILD-TYPE 64 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    1
  13Q GAIN WILD-TYPE   64   17
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 5                 64
  YES                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  13Q GAIN MUTATED                                       0
  13Q GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  13Q GAIN MUTATED                                          0
  13Q GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  13Q GAIN MUTATED                                      6
  13Q GAIN WILD-TYPE                                   79
D25V8, multiclass
                                          clus
vv                                         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    6                 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"
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED    4  0  2  0
  13Q GAIN WILD-TYPE 59  7 10  5
D25V9, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                4                 59
  R1                0                  7
  R2                2                 10
  RX                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"
D25V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         0     5
  13Q GAIN WILD-TYPE     2                         1    71
D25V11, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    1  3
  13Q GAIN WILD-TYPE  7 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    3
  13Q GAIN WILD-TYPE    7   35
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                3                 35
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   10 11
  14Q GAIN WILD-TYPE 47 22
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 69 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                 22 
$`14Q GAIN MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JA 
       91.30        39.58        68.75        13.91        12.00        30.31 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5KO 
       69.21        17.79        16.11        67.59        15.25        46.49 
TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM 
       60.89        31.79        29.10        14.33        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI 
       79.07        36.03        38.50 

$`14Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        43.30        12.59        42.51        44.55        55.13 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC 
       88.87        16.11        19.04        44.45        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JM 
       99.88        66.25        69.37        76.64        49.22        18.48 
TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       39.25        36.26       121.25        12.59        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
       66.51        72.39        31.23        18.15        27.02       108.13 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       113.92        35.57        16.37        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        68.25        44.84        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
      152.15        28.31        28.64        23.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        52.24        78.41        36.33        90.08 
TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG 
       77.00        61.05        28.04        18.05         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       20.25        39.48        22.32 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                12                  0 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             91.30             153.63 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             38.50              39.25 
[1] "12.0 - 91.3 (38.5)" "0.0 - 153.6 (39.2)"
[1] "hr=" "1.7"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         2        8         3        8
  14Q GAIN WILD-TYPE       7       35        15       10
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  2                  7
  STAGE II                 8                 35
  STAGE III                3                 15
  STAGE IV                 8                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  14Q GAIN MUTATED    2  9  2  8
  14Q GAIN WILD-TYPE  7 39  9 12
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                2                  7
  T2                9                 39
  T3                2                  9
  T4                8                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   17  4
  14Q GAIN WILD-TYPE 61  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     17    4
  14Q GAIN WILD-TYPE   61    6
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               17                 61
  1                4                  6
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   15  6
  14Q GAIN WILD-TYPE 44 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15    6
  14Q GAIN WILD-TYPE   44   25
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               15                 44
  MALE                  6                 25
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   19  1
  14Q GAIN WILD-TYPE 50 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     19    1
  14Q GAIN WILD-TYPE   50   17
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                19                 50
  YES                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  14Q GAIN MUTATED                                       0
  14Q GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  14Q GAIN MUTATED                                          0
  14Q GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  14Q GAIN MUTATED                                     21
  14Q GAIN WILD-TYPE                                   64
D26V8, multiclass
                                          clus
vv                                         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   21                 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"
                    vv
clus                 R0 R1 R2 RX
  14Q GAIN MUTATED   13  2  4  1
  14Q GAIN WILD-TYPE 50  5  8  4
D26V9, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               13                 50
  R1                2                  5
  R2                4                  8
  RX                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"
D26V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0    17
  14Q GAIN WILD-TYPE     2                         1    59
D26V11, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   17                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    3  8
  14Q GAIN WILD-TYPE  5 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    8
  14Q GAIN WILD-TYPE    5   30
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO                8                 30
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    5  6
  15Q GAIN WILD-TYPE 52 27
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 79 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                 27 
$`15Q GAIN MUTATED`
TCGA-OR-A5LB TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5KU 
       39.58        30.31        57.53        49.22        67.59       153.63 
TCGA-OR-A5KW TCGA-OR-A5L2 TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       68.25        60.89        53.03        61.08        79.07 

$`15Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        18.12        99.88        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO 
       17.79        69.37        76.64        16.11        18.48        39.25 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       15.25        36.26       121.25        12.59        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
       66.51        72.39        31.23        18.15        27.02       108.13 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       113.92        35.57        16.37        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        46.49        88.01        83.80        95.18 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
      127.50        44.84        12.85         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.35        21.76        14.63        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       36.33        90.08        77.00        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             30.31               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            153.63             152.15 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             60.89              35.57 
[1] "30.3 - 153.6 (60.9)" "0.0 - 152.2 (35.6)" 
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         1        5         1        3
  15Q GAIN WILD-TYPE       8       38        17       15
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 5                 38
  STAGE III                1                 17
  STAGE IV                 3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN MUTATED    1  6  0  3
  15Q GAIN WILD-TYPE  8 42 11 17
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                1                  8
  T2                6                 42
  T3                0                 11
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    9  1
  15Q GAIN WILD-TYPE 69  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9    1
  15Q GAIN WILD-TYPE   69    9
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                9                 69
  1                1                  9
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    7  4
  15Q GAIN WILD-TYPE 52 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7    4
  15Q GAIN WILD-TYPE   52   27
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                7                 52
  MALE                  4                 27
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    7  3
  15Q GAIN WILD-TYPE 62 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7    3
  15Q GAIN WILD-TYPE   62   15
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 7                 62
  YES                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  15Q GAIN MUTATED                                       0
  15Q GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  15Q GAIN MUTATED                                          0
  15Q GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  15Q GAIN MUTATED                                     11
  15Q GAIN WILD-TYPE                                   74
D27V8, multiclass
                                          clus
vv                                         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   11                 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"
                    vv
clus                 R0 R1 R2 RX
  15Q GAIN MUTATED    8  1  1  0
  15Q GAIN WILD-TYPE 55  6 11  5
D27V9, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                8                 55
  R1                1                  6
  R2                1                 11
  RX                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"
D27V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         0     8
  15Q GAIN WILD-TYPE     2                         1    68
D27V11, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    8                 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"
D27V12, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    0  4
  15Q GAIN WILD-TYPE  8 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    4
  15Q GAIN WILD-TYPE    8   34
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                4                 34
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   35 15
  16P GAIN WILD-TYPE 22 18
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                50                 40 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                 18 
$`16P GAIN MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 
       43.30        39.58        12.59        68.75        12.00        44.45 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       30.31        57.53        66.25        17.79        69.37        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       16.11        49.22        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       31.23        27.02       108.13       113.92        35.57        16.37 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY 
       24.62        46.49        83.80       153.63        68.25        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11        58.55        31.79        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM 
       23.64         5.23        14.63        14.33        53.03        61.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5HC 
       24.85        22.32 

$`16P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 
       33.83        91.30        42.51        44.55        55.13        13.91 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE 
       88.87        16.11        19.04        18.12        99.88        69.21 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU 
       67.59        18.48        39.25        15.25        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB 
       72.39        18.15        32.68        49.08        11.31        24.36 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 
       88.01        95.18       127.50        44.84        60.89       152.15 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        21.76        52.24        78.41        36.33        90.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-PK-A5H9 TCGA-PK-A5HA 
       77.00        79.07        20.25        39.48 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               0.0                9.5 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            153.63             152.15 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             33.68              43.53 
[1] "0.0 - 153.6 (33.7)" "9.5 - 152.2 (43.5)"
[1] "hr=" "1.3"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         3       24        10       12
  16P GAIN WILD-TYPE       6       19         8        6
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  3                  6
  STAGE II                24                 19
  STAGE III               10                  8
  STAGE IV                12                  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"
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    3 26  5 15
  16P GAIN WILD-TYPE  6 22  6  5
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                  6
  T2               26                 22
  T3                5                  6
  T4               15                  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"
D28V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   44  5
  16P GAIN WILD-TYPE 34  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     44    5
  16P GAIN WILD-TYPE   34    5
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               44                 34
  1                5                  5
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   30 20
  16P GAIN WILD-TYPE 29 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     30   20
  16P GAIN WILD-TYPE   29   11
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               30                 29
  MALE                 20                 11
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   39  9
  16P GAIN WILD-TYPE 30  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     39    9
  16P GAIN WILD-TYPE   30    9
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                39                 30
  YES                9                  9
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  16P GAIN MUTATED                                       1
  16P GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  16P GAIN MUTATED                                          2
  16P GAIN WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  16P GAIN MUTATED                                     47
  16P GAIN WILD-TYPE                                   38
D28V8, multiclass
                                          clus
vv                                         16P GAIN MUTATED 16P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   47                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED   33  4  8  3
  16P GAIN WILD-TYPE 30  3  4  2
D28V9, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               33                 30
  R1                4                  3
  R2                8                  4
  RX                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"
D28V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0    43
  16P GAIN WILD-TYPE     1                         1    33
D28V11, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   43                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3 23
  16P GAIN WILD-TYPE  5 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   23
  16P GAIN WILD-TYPE    5   15
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               23                 15
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   33 14
  16Q GAIN WILD-TYPE 24 19
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                47                 43 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                14                 19 
$`16Q GAIN MUTATED`
TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA 
       43.30        12.59        68.75        12.00        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       57.53        69.21        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       49.22        36.26       121.25        29.82        66.51        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO 
       27.02       108.13       113.92        35.57        24.62        46.49 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
       83.80       153.63        68.25        12.85         4.11        58.55 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LF TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       14.63        53.03        61.08        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG 
       36.03        18.05        38.50         0.00        24.85 

$`16Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        91.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD 
       13.91        88.87        16.11        19.04        18.12        99.88 
TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       66.25        67.59        18.48        39.25        15.25        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 
        9.50        72.39        18.15        32.68        16.37        49.08 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       11.31        24.36        88.01        95.18       127.50        44.84 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH 
       60.89       152.15        39.35        21.76        52.24        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-PK-A5H9 TCGA-PK-A5HA 
       14.33        36.33        90.08        77.00        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               0.0                9.5 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            153.63             152.15 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             36.03              39.48 
[1] "0.0 - 153.6 (36.0)" "9.5 - 152.2 (39.5)"
[1] "hr=" "1.4"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         4       24         8       10
  16Q GAIN WILD-TYPE       5       19        10        8
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  4                  5
  STAGE II                24                 19
  STAGE III                8                 10
  STAGE IV                10                  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"
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    4 26  4 12
  16Q GAIN WILD-TYPE  5 22  7  8
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                4                  5
  T2               26                 22
  T3                4                  7
  T4               12                  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"
D29V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   41  5
  16Q GAIN WILD-TYPE 37  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     41    5
  16Q GAIN WILD-TYPE   37    5
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               41                 37
  1                5                  5
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   28 19
  16Q GAIN WILD-TYPE 31 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     28   19
  16Q GAIN WILD-TYPE   31   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               28                 31
  MALE                 19                 12
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   39  6
  16Q GAIN WILD-TYPE 30 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     39    6
  16Q GAIN WILD-TYPE   30   12
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                39                 30
  YES                6                 12
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  16Q GAIN MUTATED                                       1
  16Q GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  16Q GAIN MUTATED                                          2
  16Q GAIN WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  16Q GAIN MUTATED                                     44
  16Q GAIN WILD-TYPE                                   41
D29V8, multiclass
                                          clus
vv                                         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   44                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED   32  3  7  3
  16Q GAIN WILD-TYPE 31  4  5  2
D29V9, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               32                 31
  R1                3                  4
  R2                7                  5
  RX                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"
D29V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         0    40
  16Q GAIN WILD-TYPE     2                         1    36
D29V11, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   40                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3 20
  16Q GAIN WILD-TYPE  5 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   20
  16Q GAIN WILD-TYPE    5   18
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               20                 18
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    3  2
  17P GAIN WILD-TYPE 54 31
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 85 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 31 
$`17P GAIN MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JQ TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PK-A5HC 
       19.04        36.26        18.05         0.00        22.32 

$`17P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        44.45        30.31        18.12        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       49.22        67.59        18.48        39.25        15.25       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       16.37        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       44.84        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.35        21.76        14.63        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       36.33        90.08        53.03        61.08        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 
       61.05        28.04        36.03        38.50        24.85        20.25 
TCGA-PK-A5HA 
       39.48 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.00               4.11 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             36.26             153.63 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             19.04              39.48 
[1] "0.0 - 36.3 (19.0)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "2.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED         0        1         3        1
  17P GAIN WILD-TYPE       9       42        15       17
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                3                 15
  STAGE IV                 1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17P GAIN MUTATED    0  1  2  2
  17P GAIN WILD-TYPE  9 47  9 18
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                2                  9
  T4                2                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  0
  17P GAIN WILD-TYPE 73 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    0
  17P GAIN WILD-TYPE   73   10
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                5                 73
  1                0                 10
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    3  2
  17P GAIN WILD-TYPE 56 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    2
  17P GAIN WILD-TYPE   56   29
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                3                 56
  MALE                  2                 29
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  1
  17P GAIN WILD-TYPE 65 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    1
  17P GAIN WILD-TYPE   65   17
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 4                 65
  YES                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  17P GAIN MUTATED                                       1
  17P GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  17P GAIN MUTATED                                          0
  17P GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  17P GAIN MUTATED                                      4
  17P GAIN WILD-TYPE                                   81
D30V8, multiclass
                                          clus
vv                                         17P GAIN MUTATED 17P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    4                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  17P GAIN MUTATED    3  1  1  0
  17P GAIN WILD-TYPE 60  6 11  5
D30V9, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                3                 60
  R1                1                  6
  R2                1                 11
  RX                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"
D30V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       1                         0     3
  17P GAIN WILD-TYPE     1                         1    73
D30V11, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    1  2
  17P GAIN WILD-TYPE  7 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    2
  17P GAIN WILD-TYPE    7   36
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 36
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    3  4
  17Q GAIN WILD-TYPE 54 29
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 83 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                 29 
$`17Q GAIN MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5L2 TCGA-OR-A5LI TCGA-OR-A5LT 
       19.04        69.37        36.26        60.89        14.33        18.05 
TCGA-P6-A5OH 
        0.00 

$`17Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        44.45        30.31        18.12        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       69.21        66.25        17.79        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS 
       67.59        18.48        39.25        15.25       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.08        24.62        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       12.85         4.11        58.55       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50        24.85        20.25        39.48        22.32 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.00               4.11 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             69.37             153.63 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             19.04              39.35 
[1] "0.0 - 69.4 (19.0)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "2.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED         0        3         2        2
  17Q GAIN WILD-TYPE       9       40        16       16
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 3                 40
  STAGE III                2                 16
  STAGE IV                 2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED    0  3  2  2
  17Q GAIN WILD-TYPE  9 45  9 18
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                0                  9
  T2                3                 45
  T3                2                  9
  T4                2                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    7  0
  17Q GAIN WILD-TYPE 71 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7    0
  17Q GAIN WILD-TYPE   71   10
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                7                 71
  1                0                 10
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    5  2
  17Q GAIN WILD-TYPE 54 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    2
  17Q GAIN WILD-TYPE   54   29
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                5                 54
  MALE                  2                 29
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    6  1
  17Q GAIN WILD-TYPE 63 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6    1
  17Q GAIN WILD-TYPE   63   17
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 6                 63
  YES                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  17Q GAIN MUTATED                                       1
  17Q GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  17Q GAIN MUTATED                                          1
  17Q GAIN WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  17Q GAIN MUTATED                                      5
  17Q GAIN WILD-TYPE                                   80
D31V8, multiclass
                                          clus
vv                                         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                1                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    5                 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"
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED    5  0  2  0
  17Q GAIN WILD-TYPE 58  7 10  5
D31V9, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                5                 58
  R1                0                  7
  R2                2                 10
  RX                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"
D31V10, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 29 
        TCGA-OR-A5KP         TCGA-P6-A5OG         TCGA-OR-A5J2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-OR-A5J3         TCGA-OR-A5J4         TCGA-OR-A5J7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-OR-A5JG         TCGA-OR-A5JJ         TCGA-OR-A5JT 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JX         TCGA-OR-A5JY 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K5         TCGA-OR-A5KB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-OR-A5KY         TCGA-OR-A5L9         TCGA-OR-A5LG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LM         TCGA-OR-A5LN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-OR-A5LO         TCGA-OR-A5LP         TCGA-OU-A5PI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-PK-A5HA         TCGA-PK-A5HC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         0     6
  17Q GAIN WILD-TYPE     2                         1    70
D31V11, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    6                 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"
D31V12, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    1  3
  17Q GAIN WILD-TYPE  7 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    3
  17Q GAIN WILD-TYPE    7   35
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                3                 35
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    2  4
  18P GAIN WILD-TYPE 55 29
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 84 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 29 
$`18P GAIN MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-PK-A5HC 
       19.04        58.55        60.89        39.35        14.33        22.32 

$`18P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        44.45        30.31        18.12        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        67.59        18.48        39.25        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       35.57        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
       68.25        44.84        12.85         4.11       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LE 
       28.31        29.10        28.64        23.64         5.23        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             14.33               0.00 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             60.89             153.63 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            30.835             38.875 
[1] "14.3 - 60.9 (30.8)" "0.0 - 153.6 (38.9)"
[1] "hr=" "2.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         0        2         3        1
  18P GAIN WILD-TYPE       9       41        15       17
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 2                 41
  STAGE III                3                 15
  STAGE IV                 1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18P GAIN MUTATED    0  2  1  3
  18P GAIN WILD-TYPE  9 46 10 17
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                  9
  T2                2                 46
  T3                1                 10
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    6  0
  18P GAIN WILD-TYPE 72 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    0
  18P GAIN WILD-TYPE   72   10
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                6                 72
  1                0                 10
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  2
  18P GAIN WILD-TYPE 55 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    2
  18P GAIN WILD-TYPE   55   29
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                 55
  MALE                  2                 29
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    5  1
  18P GAIN WILD-TYPE 64 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    1
  18P GAIN WILD-TYPE   64   17
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 5                 64
  YES                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  18P GAIN MUTATED                                       0
  18P GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  18P GAIN MUTATED                                          0
  18P GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  18P GAIN MUTATED                                      6
  18P GAIN WILD-TYPE                                   79
D32V8, multiclass
                                          clus
vv                                         18P GAIN MUTATED 18P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    6                 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"
                    vv
clus                 R0 R1 R2 RX
  18P GAIN MUTATED    3  1  1  1
  18P GAIN WILD-TYPE 60  6 11  4
D32V9, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                3                 60
  R1                1                  6
  R2                1                 11
  RX                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"
D32V10, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 29 
        TCGA-OR-A5KP         TCGA-P6-A5OG         TCGA-OR-A5J2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-OR-A5J3         TCGA-OR-A5J4         TCGA-OR-A5J7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-OR-A5JG         TCGA-OR-A5JJ         TCGA-OR-A5JT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JX         TCGA-OR-A5JY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K5         TCGA-OR-A5KB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-OR-A5KY         TCGA-OR-A5L9         TCGA-OR-A5LG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LM         TCGA-OR-A5LN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-OR-A5LO         TCGA-OR-A5LP         TCGA-OR-A5LT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-OU-A5PI         TCGA-PK-A5HA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         0     5
  18P GAIN WILD-TYPE     1                         1    71
D32V11, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  5
  18P GAIN WILD-TYPE  7 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    5
  18P GAIN WILD-TYPE    7   33
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                5                 33
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    2  3
  18Q GAIN WILD-TYPE 55 30
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 85 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 30 
$`18Q GAIN MUTATED`
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-PK-A5HC 
       58.55        60.89        39.35        14.33        22.32 

$`18Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        44.45        30.31        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       99.88        69.21        66.25        17.79        69.37        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       16.11        49.22        67.59        18.48        39.25        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       72.39        31.23        18.15        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      113.92        35.57        16.37        49.08        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      127.50        68.25        44.84        12.85         4.11       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        52.24        78.41        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        38.50         0.00        24.85        20.25 
TCGA-PK-A5HA 
       39.48 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             14.33               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             60.89             153.63 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             39.35              38.50 
[1] "14.3 - 60.9 (39.4)" "0.0 - 153.6 (38.5)"
[1] "hr=" "1.8"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         0        2         2        1
  18Q GAIN WILD-TYPE       9       41        16       17
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 2                 41
  STAGE III                2                 16
  STAGE IV                 1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN MUTATED    0  2  0  3
  18Q GAIN WILD-TYPE  9 46 11 17
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                  9
  T2                2                 46
  T3                0                 11
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  0
  18Q GAIN WILD-TYPE 73 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    0
  18Q GAIN WILD-TYPE   73   10
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                5                 73
  1                0                 10
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  1
  18Q GAIN WILD-TYPE 55 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    1
  18Q GAIN WILD-TYPE   55   30
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                 55
  MALE                  1                 30
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  0
  18Q GAIN WILD-TYPE 64 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    0
  18Q GAIN WILD-TYPE   64   18
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 5                 64
  YES                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  18Q GAIN MUTATED                                       0
  18Q GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  18Q GAIN MUTATED                                          0
  18Q GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  18Q GAIN MUTATED                                      5
  18Q GAIN WILD-TYPE                                   80
D33V8, multiclass
                                          clus
vv                                         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    5                 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"
                    vv
clus                 R0 R1 R2 RX
  18Q GAIN MUTATED    2  1  1  1
  18Q GAIN WILD-TYPE 61  6 11  4
D33V9, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                2                 61
  R1                1                  6
  R2                1                 11
  RX                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"
D33V10, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 30 
        TCGA-OR-A5KP         TCGA-P6-A5OG         TCGA-OR-A5J2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-OR-A5J3         TCGA-OR-A5J4         TCGA-OR-A5J7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-OR-A5J8         TCGA-OR-A5JG         TCGA-OR-A5JJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-OR-A5JT         TCGA-OR-A5JV         TCGA-OR-A5JX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-OR-A5JY         TCGA-OR-A5K2         TCGA-OR-A5K5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-OR-A5KB         TCGA-OR-A5KU         TCGA-OR-A5KV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-OR-A5KW         TCGA-OR-A5KY         TCGA-OR-A5L9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-OR-A5LG         TCGA-OR-A5LL         TCGA-OR-A5LM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-OR-A5LN         TCGA-OR-A5LO         TCGA-OR-A5LP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-OR-A5LT         TCGA-OU-A5PI         TCGA-PK-A5HA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       1                         0     4
  18Q GAIN WILD-TYPE     1                         1    72
D33V11, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    0  5
  18Q GAIN WILD-TYPE  8 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    5
  18Q GAIN WILD-TYPE    8   33
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                5                 33
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   32 24
  19P GAIN WILD-TYPE 25  9
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                 34 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                24                  9 
$`19P GAIN MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       33.83        91.30        39.58        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       12.00        88.87        16.11        44.45        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV 
       49.22        18.48        15.25        36.26       121.25        66.51 
TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       31.23        32.68       113.92        16.37        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ 
       46.49        83.80       153.63        68.25        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LC TCGA-OR-A5LD 
       58.55        60.89        31.79        29.10         5.23        39.35 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        90.08        53.03        61.08        77.00 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       79.07        61.05        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5HC 
       24.85        22.32 

$`19P GAIN WILD-TYPE`
TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J8 TCGA-OR-A5JB 
       43.30        12.59        42.51        44.55        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       99.88        67.59        39.25        12.59        29.82         9.50 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 
       72.39        18.15        27.02       108.13        35.57        49.08 
TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 
       24.36        88.01        95.18       127.50        44.84       152.15 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       28.31        28.64        23.64        21.76        14.63        52.24 
TCGA-OR-A5LI TCGA-OR-A5LR TCGA-PK-A5H9 TCGA-PK-A5HA 
       14.33        28.04        20.25        39.48 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               0.0                9.5 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            153.63             152.15 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            39.465             32.695 
[1] "0.0 - 153.6 (39.5)" "9.5 - 152.2 (32.7)"
[1] "hr=" "1.5"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         3       27        11       14
  19P GAIN WILD-TYPE       6       16         7        4
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  3                  6
  STAGE II                27                 16
  STAGE III               11                  7
  STAGE IV                14                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED    3 30  7 15
  19P GAIN WILD-TYPE  6 18  4  5
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                3                  6
  T2               30                 18
  T3                7                  4
  T4               15                  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"
D34V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   48  7
  19P GAIN WILD-TYPE 30  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     48    7
  19P GAIN WILD-TYPE   30    3
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               48                 30
  1                7                  3
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   36 20
  19P GAIN WILD-TYPE 23 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     36   20
  19P GAIN WILD-TYPE   23   11
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               36                 23
  MALE                 20                 11
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   46  8
  19P GAIN WILD-TYPE 23 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     46    8
  19P GAIN WILD-TYPE   23   10
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                46                 23
  YES                8                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  19P GAIN MUTATED                                       1
  19P GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  19P GAIN MUTATED                                          3
  19P GAIN WILD-TYPE                                        1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  19P GAIN MUTATED                                     52
  19P GAIN WILD-TYPE                                   33
D34V8, multiclass
                                          clus
vv                                         19P GAIN MUTATED 19P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                3                  1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   52                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED   37  5  9  3
  19P GAIN WILD-TYPE 26  2  3  2
D34V9, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               37                 26
  R1                5                  2
  R2                9                  3
  RX                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"
D34V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         1    46
  19P GAIN WILD-TYPE     1                         0    30
D34V11, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   46                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    7 21
  19P GAIN WILD-TYPE  1 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   21
  19P GAIN WILD-TYPE    1   17
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                  1
  NOT HISPANIC OR LATINO               21                 17
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   30 22
  19Q GAIN WILD-TYPE 27 11
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                52                 38 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                 11 
$`19Q GAIN MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 
       91.30        39.58        55.13        68.75        13.91        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE 
       88.87        16.11        44.45        30.31        57.53        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       66.25        17.79        69.37        76.64        16.11        49.22 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K2 
       15.25        36.26       121.25        66.51        31.23        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KS TCGA-OR-A5KU 
      113.92        16.37        24.62        11.31        83.80       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 
       68.25        44.84        12.85         4.11        58.55        31.79 
TCGA-OR-A5L8 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       29.10         5.23        39.35        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT 
       90.08        61.08        79.07        61.05        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5HC 
       38.50         0.00        24.85        22.32 

$`19Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J8 
       33.83        43.30        12.59        42.51        44.55        19.04 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS 
       18.12        99.88        67.59        18.48        39.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
       29.82         9.50        72.39        18.15        27.02       108.13 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT 
       35.57        49.08        24.36        46.49        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      127.50        60.89       152.15        28.31        28.64        23.64 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LR 
       21.76        14.63        52.24        53.03        77.00        28.04 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               0.0                9.5 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            153.63             152.15 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            38.925             37.410 
[1] "0.0 - 153.6 (38.9)" "9.5 - 152.2 (37.4)"
[1] "hr=" "1.4"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         3       23        12       13
  19Q GAIN WILD-TYPE       6       20         6        5
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  3                  6
  STAGE II                23                 20
  STAGE III               12                  6
  STAGE IV                13                  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                 T1 T2 T3 T4
  19Q GAIN MUTATED    3 27  7 14
  19Q GAIN WILD-TYPE  6 21  4  6
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                3                  6
  T2               27                 21
  T3                7                  4
  T4               14                  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"
D35V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   43  8
  19Q GAIN WILD-TYPE 35  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     43    8
  19Q GAIN WILD-TYPE   35    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               43                 35
  1                8                  2
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   32 20
  19Q GAIN WILD-TYPE 27 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     32   20
  19Q GAIN WILD-TYPE   27   11
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               32                 27
  MALE                 20                 11
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   43  7
  19Q GAIN WILD-TYPE 26 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     43    7
  19Q GAIN WILD-TYPE   26   11
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                43                 26
  YES                7                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  19Q GAIN MUTATED                                       1
  19Q GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  19Q GAIN MUTATED                                          3
  19Q GAIN WILD-TYPE                                        1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  19Q GAIN MUTATED                                     48
  19Q GAIN WILD-TYPE                                   37
D35V8, multiclass
                                          clus
vv                                         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                3                  1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   48                 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"
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED   33  4 10  3
  19Q GAIN WILD-TYPE 30  3  2  2
D35V9, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               33                 30
  R1                4                  3
  R2               10                  2
  RX                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"
D35V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         1    44
  19Q GAIN WILD-TYPE     1                         0    32
D35V11, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   44                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    7 21
  19Q GAIN WILD-TYPE  1 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      7   21
  19Q GAIN WILD-TYPE    1   17
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                  1
  NOT HISPANIC OR LATINO               21                 17
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   33 13
  20P GAIN WILD-TYPE 24 20
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                46                 44 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                 20 
$`20P GAIN MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J9 
       43.30        39.58        55.13        13.91        88.87        44.45 
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       57.53        69.21        66.25        17.79        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       49.22        36.26       121.25        29.82        66.51        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KS 
       27.02       108.13       113.92        35.57        24.62        83.80 
TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 
      153.63        44.84        12.85         4.11        58.55        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LI 
       28.31        28.64        23.64         5.23        14.63        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        90.08        61.08        77.00        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG 
       36.03        18.05         0.00        24.85 

$`20P GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       33.83        91.30        12.59        42.51        44.55        68.75 
TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       12.00        16.11        19.04        30.31        18.12        99.88 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       16.11        67.59        18.48        39.25        15.25        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 
        9.50        72.39        18.15        32.68        16.37        49.08 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV 
       11.31        24.36        46.49        88.01        95.18       127.50 
TCGA-OR-A5KW TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L8 TCGA-OR-A5LD TCGA-OR-A5LE 
       68.25        60.89       152.15        29.10        39.35        21.76 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OU-A5PI TCGA-PK-A5H9 
       52.24        78.41        53.03        79.07        38.50        20.25 
TCGA-PK-A5HA TCGA-PK-A5HC 
       39.48        22.32 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               0.0                9.5 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            153.63             152.15 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            37.955             38.875 
[1] "0.0 - 153.6 (38.0)" "9.5 - 152.2 (38.9)"
[1] "hr=" "1.7"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         4       25         6       10
  20P GAIN WILD-TYPE       5       18        12        8
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  4                  5
  STAGE II                25                 18
  STAGE III                6                 12
  STAGE IV                10                  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"
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED    4 27  5  9
  20P GAIN WILD-TYPE  5 21  6 11
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                4                  5
  T2               27                 21
  T3                5                  6
  T4                9                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   40  5
  20P GAIN WILD-TYPE 38  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     40    5
  20P GAIN WILD-TYPE   38    5
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               40                 38
  1                5                  5
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   27 19
  20P GAIN WILD-TYPE 32 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     27   19
  20P GAIN WILD-TYPE   32   12
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               27                 32
  MALE                 19                 12
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   37  7
  20P GAIN WILD-TYPE 32 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     37    7
  20P GAIN WILD-TYPE   32   11
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                37                 32
  YES                7                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  20P GAIN MUTATED                                       1
  20P GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  20P GAIN MUTATED                                          3
  20P GAIN WILD-TYPE                                        1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  20P GAIN MUTATED                                     42
  20P GAIN WILD-TYPE                                   43
D36V8, multiclass
                                          clus
vv                                         20P GAIN MUTATED 20P GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                3                  1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   42                 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"
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   32  2  8  3
  20P GAIN WILD-TYPE 31  5  4  2
D36V9, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               32                 31
  R1                2                  5
  R2                8                  4
  RX                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"
D36V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         1    38
  20P GAIN WILD-TYPE     2                         0    38
D36V11, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   38                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    4 19
  20P GAIN WILD-TYPE  4 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4   19
  20P GAIN WILD-TYPE    4   19
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               19                 19
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   33 16
  20Q GAIN WILD-TYPE 24 17
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                49                 41 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                16                 17 
$`20Q GAIN MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J8 
       43.30        39.58        55.13        13.91        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       44.45        57.53        69.21        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       76.64        16.11        49.22        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       66.51        31.23        27.02       108.13       113.92        35.57 
TCGA-OR-A5K8 TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
       24.62       153.63        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       60.89        31.79        28.31        28.64        23.64         5.23 
TCGA-OR-A5LF TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       14.63        14.33        36.33        90.08        61.08        77.00 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG 
       24.85 

$`20Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J3 
       33.83        91.30        12.59        42.51        44.55        68.75 
TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL 
       12.00        16.11        30.31        18.12        99.88        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW 
       18.48        39.25        15.25        12.59         9.50        72.39 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB 
       18.15        32.68        16.37        49.08        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        88.01        83.80        95.18       127.50        68.25 
TCGA-OR-A5L3 TCGA-OR-A5L8 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH 
      152.15        29.10        39.35        21.76        52.24        78.41 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       53.03        79.07        20.25        39.48        22.32 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               0.0                9.5 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            153.63             152.15 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             36.33              39.35 
[1] "0.0 - 153.6 (36.3)" "9.5 - 152.2 (39.4)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         4       25         7       12
  20Q GAIN WILD-TYPE       5       18        11        6
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  4                  5
  STAGE II                25                 18
  STAGE III                7                 11
  STAGE IV                12                  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"
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED    4 28  6 10
  20Q GAIN WILD-TYPE  5 20  5 10
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                4                  5
  T2               28                 20
  T3                6                  5
  T4               10                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   41  7
  20Q GAIN WILD-TYPE 37  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     41    7
  20Q GAIN WILD-TYPE   37    3
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               41                 37
  1                7                  3
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   29 20
  20Q GAIN WILD-TYPE 30 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     29   20
  20Q GAIN WILD-TYPE   30   11
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               29                 30
  MALE                 20                 11
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   39  8
  20Q GAIN WILD-TYPE 30 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     39    8
  20Q GAIN WILD-TYPE   30   10
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                39                 30
  YES                8                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  20Q GAIN MUTATED                                       1
  20Q GAIN WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  20Q GAIN MUTATED                                          3
  20Q GAIN WILD-TYPE                                        1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  20Q GAIN MUTATED                                     45
  20Q GAIN WILD-TYPE                                   40
D37V8, multiclass
                                          clus
vv                                         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                3                  1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   45                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED   33  2  9  3
  20Q GAIN WILD-TYPE 30  5  3  2
D37V9, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               33                 30
  R1                2                  5
  R2                9                  3
  RX                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"
D37V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       0                         1    41
  20Q GAIN WILD-TYPE     2                         0    35
D37V11, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   41                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    5 20
  20Q GAIN WILD-TYPE  3 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5   20
  20Q GAIN WILD-TYPE    3   18
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  3
  NOT HISPANIC OR LATINO               20                 18
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   18 13
  21Q GAIN WILD-TYPE 39 20
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                 59 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                 20 
$`21Q GAIN MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J6 
       33.83        91.30        39.58        44.55        68.75        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JI 
       16.11        44.45        57.53        69.21        17.79        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JX TCGA-OR-A5K9 TCGA-OR-A5KB 
       16.11        49.22        67.59        31.23        11.31        24.36 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63        68.25        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5LA TCGA-OR-A5LI TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS 
       60.89        23.64        14.33        61.08        79.07        36.03 
TCGA-OU-A5PI 
       38.50 

$`21Q GAIN WILD-TYPE`
TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 
       43.30        12.59        42.51        55.13        13.91        12.00 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        30.31        18.12        99.88        66.25        69.37 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       18.48        39.25        15.25        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       29.82         9.50        66.51        72.39        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
      108.13        32.68       113.92        35.57        16.37        49.08 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV 
       24.62        46.49        88.01        83.80        95.18       127.50 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LC 
      152.15        31.79        28.31        29.10        28.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.35        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       90.08        53.03        77.00        61.05        28.04        18.05 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
        0.00        24.85        20.25        39.48        22.32 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              4.11               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            153.63             152.15 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             44.55              35.57 
[1] "4.1 - 153.6 (44.5)" "0.0 - 152.2 (35.6)"
[1] "hr=" "1.2"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         3       15         5        7
  21Q GAIN WILD-TYPE       6       28        13       11
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  3                  6
  STAGE II                15                 28
  STAGE III                5                 13
  STAGE IV                 7                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q GAIN MUTATED    3 18  3  6
  21Q GAIN WILD-TYPE  6 30  8 14
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                  6
  T2               18                 30
  T3                3                  8
  T4                6                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   24  6
  21Q GAIN WILD-TYPE 54  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     24    6
  21Q GAIN WILD-TYPE   54    4
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               24                 54
  1                6                  4
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   21 10
  21Q GAIN WILD-TYPE 38 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     21   10
  21Q GAIN WILD-TYPE   38   21
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               21                 38
  MALE                 10                 21
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   25  4
  21Q GAIN WILD-TYPE 44 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     25    4
  21Q GAIN WILD-TYPE   44   14
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                25                 44
  YES                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  21Q GAIN MUTATED                                       0
  21Q GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  21Q GAIN MUTATED                                          0
  21Q GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  21Q GAIN MUTATED                                     31
  21Q GAIN WILD-TYPE                                   54
D38V8, multiclass
                                          clus
vv                                         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   31                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  21Q GAIN MUTATED   22  2  4  1
  21Q GAIN WILD-TYPE 41  5  8  4
D38V9, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               22                 41
  R1                2                  5
  R2                4                  8
  RX                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"
D38V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         1    27
  21Q GAIN WILD-TYPE     2                         0    49
D38V11, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   27                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    4 13
  21Q GAIN WILD-TYPE  4 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   13
  21Q GAIN WILD-TYPE    4   25
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               13                 25
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    0  3
  22Q GAIN WILD-TYPE 57 30
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 87 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 30 
$`22Q GAIN MUTATED`
TCGA-OR-A5JJ TCGA-OR-A5L2 TCGA-OR-A5LH 
       16.11        60.89        78.41 

$`22Q GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        44.45        30.31        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       99.88        69.21        66.25        17.79        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        67.59        18.48        39.25        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       35.57        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
       68.25        44.84        12.85         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LJ 
       39.35        21.76        14.63        52.24        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       90.08        53.03        61.08        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG 
       28.04        36.03        18.05        38.50         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       20.25        39.48        22.32 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             16.11               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             78.41             153.63 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             60.89              38.50 
[1] "16.1 - 78.4 (60.9)" "0.0 - 153.6 (38.5)"
[1] "hr=" "2.4"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         0        2         0        1
  22Q GAIN WILD-TYPE       9       41        18       17
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 2                 41
  STAGE III                0                 18
  STAGE IV                 1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  22Q GAIN MUTATED    0  2  0  1
  22Q GAIN WILD-TYPE  9 46 11 19
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                0                  9
  T2                2                 46
  T3                0                 11
  T4                1                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2  1
  22Q GAIN WILD-TYPE 76  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    1
  22Q GAIN WILD-TYPE   76    9
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                2                 76
  1                1                  9
[1] 2 2
[1] FALSE
D39V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2  1
  22Q GAIN WILD-TYPE 57 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    1
  22Q GAIN WILD-TYPE   57   30
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 30
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    3  0
  22Q GAIN WILD-TYPE 66 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    0
  22Q GAIN WILD-TYPE   66   18
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 3                 66
  YES                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  22Q GAIN MUTATED                                       0
  22Q GAIN WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  22Q GAIN MUTATED                                          0
  22Q GAIN WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  22Q GAIN MUTATED                                      3
  22Q GAIN WILD-TYPE                                   82
D39V8, multiclass
                                          clus
vv                                         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    3                 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"
                    vv
clus                 R0 R1 R2 RX
  22Q GAIN MUTATED    2  0  1  0
  22Q GAIN WILD-TYPE 61  7 11  5
D39V9, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                2                 61
  R1                0                  7
  R2                1                 11
  RX                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"
D39V10, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 30 
        TCGA-OR-A5KP         TCGA-P6-A5OG         TCGA-OR-A5J2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OR-A5J3         TCGA-OR-A5J4         TCGA-OR-A5J7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OR-A5J8         TCGA-OR-A5JG         TCGA-OR-A5JT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JX         TCGA-OR-A5JY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K5         TCGA-OR-A5KB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OR-A5KU         TCGA-OR-A5KV         TCGA-OR-A5KW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OR-A5KY         TCGA-OR-A5L9         TCGA-OR-A5LG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OR-A5LL         TCGA-OR-A5LM         TCGA-OR-A5LN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OR-A5LO         TCGA-OR-A5LP         TCGA-OR-A5LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI         TCGA-PK-A5HA         TCGA-PK-A5HC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         0     3
  22Q GAIN WILD-TYPE     2                         1    73
D39V11, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    0  2
  22Q GAIN WILD-TYPE  8 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    2
  22Q GAIN WILD-TYPE    8   36
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 36
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED   27 16
  XP GAIN WILD-TYPE 30 17
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               43                47 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               16                17 
$`XP GAIN MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 
       43.30        39.58        55.13        68.75        13.91        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       88.87        19.04        44.45        69.21        66.25        16.11 
TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
       67.59       121.25        29.82        18.15        27.02       108.13 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU 
      113.92        35.57        24.62        46.49        83.80       153.63 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 
       68.25        12.85         4.11        58.55        60.89        31.79 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH 
       29.10        28.64        23.64        39.35        14.63        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       36.33        61.08        79.07        61.05        28.04        18.05 
TCGA-PA-A5YG 
       24.85 

$`XP GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J7 
       33.83        91.30        12.59        42.51        44.55        16.11 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       30.31        18.12        57.53        99.88        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       76.64        49.22        18.48        39.25        15.25        36.26 
TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 
       12.59         9.50        66.51        72.39        31.23        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT 
       16.37        49.08        11.31        24.36        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE 
      127.50        44.84       152.15        28.31         5.23        21.76 
TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS 
       52.24        14.33        90.08        53.03        77.00        36.03 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50         0.00        20.25        39.48        22.32 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             4.11              0.00 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           153.63            152.15 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            39.58             36.26 
[1] "4.1 - 153.6 (39.6)" "0.0 - 152.2 (36.3)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED         4       22         9        8
  XP GAIN WILD-TYPE       5       21         9       10
D40V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 4                 5
  STAGE II               22                21
  STAGE III               9                 9
  STAGE IV                8                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XP GAIN MUTATED    4 24  6  9
  XP GAIN WILD-TYPE  5 24  5 11
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               4                 5
  T2              24                24
  T3               6                 5
  T4               9                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   37  6
  XP GAIN WILD-TYPE 41  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     37    6
  XP GAIN WILD-TYPE   41    4
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              37                41
  1               6                 4
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   28 15
  XP GAIN WILD-TYPE 31 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     28   15
  XP GAIN WILD-TYPE   31   16
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              28                31
  MALE                15                16
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   35  8
  XP GAIN WILD-TYPE 34 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     35    8
  XP GAIN WILD-TYPE   34   10
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               35                34
  YES               8                10
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  XP GAIN MUTATED                                       0
  XP GAIN WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  XP GAIN MUTATED                                          1
  XP GAIN WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  XP GAIN MUTATED                                     42
  XP GAIN WILD-TYPE                                   43
D40V8, multiclass
                                          clus
vv                                         XP GAIN MUTATED XP GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  42                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"
                   vv
clus                R0 R1 R2 RX
  XP GAIN MUTATED   31  1  7  4
  XP GAIN WILD-TYPE 32  6  5  1
D40V9, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              31                32
  R1               1                 6
  R2               7                 5
  RX               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"
D40V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         1    37
  XP GAIN WILD-TYPE     2                         0    39
D40V11, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  37                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    7 20
  XP GAIN WILD-TYPE  1 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7   20
  XP GAIN WILD-TYPE    1   18
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              20                18
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   27 14
  XQ GAIN WILD-TYPE 30 19
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               41                49 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               14                19 
$`XQ GAIN MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 
       43.30        39.58        55.13        68.75        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       19.04        44.45        69.21        66.25        16.11        67.59 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
      121.25        29.82        18.15        27.02       108.13       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU 
       35.57        24.62        24.36        46.49        83.80       153.63 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 
       12.85         4.11        58.55        31.79        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LM 
       23.64        39.35        14.63        78.41        36.33        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG 
       79.07        61.05        28.04        18.05        24.85 

$`XQ GAIN WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J4 
       33.83        91.30        12.59        42.51        44.55        13.91 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG 
       16.11        30.31        18.12        57.53        99.88        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       69.37        76.64        49.22        18.48        39.25        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26        12.59         9.50        66.51        72.39        31.23 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KQ TCGA-OR-A5KT 
       32.68        16.37        49.08        11.31        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L6 
      127.50        68.25        44.84        60.89       152.15        28.31 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LL 
        5.23        21.76        52.24        14.33        90.08        53.03 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA 
       77.00        36.03        38.50         0.00        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             4.11              0.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           153.63            152.15 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            39.35             38.50 
[1] "4.1 - 153.6 (39.4)" "0.0 - 152.2 (38.5)"
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         4       22         8        7
  XQ GAIN WILD-TYPE       5       21        10       11
D41V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 4                 5
  STAGE II               22                21
  STAGE III               8                10
  STAGE IV                7                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED    4 23  5  9
  XQ GAIN WILD-TYPE  5 25  6 11
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               4                 5
  T2              23                25
  T3               5                 6
  T4               9                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   37  4
  XQ GAIN WILD-TYPE 41  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     37    4
  XQ GAIN WILD-TYPE   41    6
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              37                41
  1               4                 6
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   26 15
  XQ GAIN WILD-TYPE 33 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     26   15
  XQ GAIN WILD-TYPE   33   16
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              26                33
  MALE                15                16
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   34  7
  XQ GAIN WILD-TYPE 35 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     34    7
  XQ GAIN WILD-TYPE   35   11
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               34                35
  YES               7                11
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  XQ GAIN MUTATED                                       0
  XQ GAIN WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  XQ GAIN MUTATED                                          1
  XQ GAIN WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  XQ GAIN MUTATED                                     40
  XQ GAIN WILD-TYPE                                   45
D41V8, multiclass
                                          clus
vv                                         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  40                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  XQ GAIN MUTATED   30  1  6  4
  XQ GAIN WILD-TYPE 33  6  6  1
D41V9, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              30                33
  R1               1                 6
  R2               6                 6
  RX               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"
D41V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         1    35
  XQ GAIN WILD-TYPE     2                         0    41
D41V11, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  35                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    6 19
  XQ GAIN WILD-TYPE  2 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6   19
  XQ GAIN WILD-TYPE    2   19
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO              19                19
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   19 10
  1P LOSS WILD-TYPE 38 23
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               29                61 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               10                23 
$`1P LOSS MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5J7 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI 
       33.83        16.11        57.53        99.88        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW 
       49.22        18.48        36.26        12.59        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KX 
       31.23        18.15        32.68        16.37        49.08        44.84 
TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL 
       60.89        28.31         5.23        52.24        14.33        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       61.08        77.00        36.03        38.50        39.48 

$`1P LOSS WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       91.30        43.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       55.13        68.75        13.91        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        30.31        18.12        69.21        66.25        17.79 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       16.11        67.59        39.25        15.25       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 
        9.50        27.02       108.13       113.92        35.57        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        68.25        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD 
      152.15        31.79        29.10        28.64        23.64        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO 
       21.76        14.63        78.41        36.33        90.08        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       61.05        28.04        18.05         0.00        24.85        20.25 
TCGA-PK-A5HC 
       22.32 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             5.23              0.00 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            99.88            153.63 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            39.48             36.33 
[1] "5.2 - 99.9 (39.5)"  "0.0 - 153.6 (36.3)"
[1] "hr=" "1"  
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         2       14         6        6
  1P LOSS WILD-TYPE       7       29        12       12
D42V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 2                 7
  STAGE II               14                29
  STAGE III               6                12
  STAGE IV                6                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED    2 16  4  6
  1P LOSS WILD-TYPE  7 32  7 14
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               2                 7
  T2              16                32
  T3               4                 7
  T4               6                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   25  3
  1P LOSS WILD-TYPE 53  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     25    3
  1P LOSS WILD-TYPE   53    7
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              25                53
  1               3                 7
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   19 10
  1P LOSS WILD-TYPE 40 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     19   10
  1P LOSS WILD-TYPE   40   21
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              19                40
  MALE                10                21
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   20  8
  1P LOSS WILD-TYPE 49 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     20    8
  1P LOSS WILD-TYPE   49   10
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               20                49
  YES               8                10
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  1P LOSS MUTATED                                       1
  1P LOSS WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  1P LOSS MUTATED                                          2
  1P LOSS WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  1P LOSS MUTATED                                     26
  1P LOSS WILD-TYPE                                   59
D42V8, multiclass
                                          clus
vv                                         1P LOSS MUTATED 1P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               2                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  26                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   20  2  4  1
  1P LOSS WILD-TYPE 43  5  8  4
D42V9, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              20                43
  R1               2                 5
  R2               4                 8
  RX               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"
D42V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         0    24
  1P LOSS WILD-TYPE     2                         1    52
D42V11, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  24                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  8
  1P LOSS WILD-TYPE  7 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    8
  1P LOSS WILD-TYPE    7   30
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               8                30
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   13  8
  1Q LOSS WILD-TYPE 44 25
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21                69 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8                25 
$`1Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       16.11        57.53        99.88        69.37        76.64        49.22 
TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       18.48        36.26        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LG 
       32.68        44.84        60.89        28.31         5.23        52.24 
TCGA-OR-A5LI TCGA-OR-A5LM TCGA-OU-A5PI 
       14.33        61.08        38.50 

$`1Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        30.31        18.12        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       17.79        16.11        67.59        39.25        15.25       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
       12.59        29.82         9.50        27.02       108.13       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       35.57        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 
       68.25        12.85         4.11        58.55       152.15        31.79 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       29.10        28.64        23.64        39.35        21.76        14.63 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        36.33        90.08        53.03        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG 
       61.05        28.04        36.03        18.05         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       20.25        39.48        22.32 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             5.23              0.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            99.88            153.63 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            44.84             36.33 
[1] "5.2 - 99.9 (44.8)"  "0.0 - 153.6 (36.3)"
[1] "hr=" "1"  
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED         1        8         5        6
  1Q LOSS WILD-TYPE       8       35        13       12
D43V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                8                35
  STAGE III               5                13
  STAGE IV                6                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1Q LOSS MUTATED    1 10  3  6
  1Q LOSS WILD-TYPE  8 38  8 14
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               1                 8
  T2              10                38
  T3               3                 8
  T4               6                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   17  3
  1Q LOSS WILD-TYPE 61  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     17    3
  1Q LOSS WILD-TYPE   61    7
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              17                61
  1               3                 7
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   12  9
  1Q LOSS WILD-TYPE 47 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     12    9
  1Q LOSS WILD-TYPE   47   22
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              12                47
  MALE                 9                22
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   14  6
  1Q LOSS WILD-TYPE 55 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14    6
  1Q LOSS WILD-TYPE   55   12
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               14                55
  YES               6                12
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  1Q LOSS MUTATED                                       1
  1Q LOSS WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  1Q LOSS MUTATED                                          2
  1Q LOSS WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  1Q LOSS MUTATED                                     18
  1Q LOSS WILD-TYPE                                   67
D43V8, multiclass
                                          clus
vv                                         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               2                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  18                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"
                   vv
clus                R0 R1 R2 RX
  1Q LOSS MUTATED   12  2  4  1
  1Q LOSS WILD-TYPE 51  5  8  4
D43V9, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              12                51
  R1               2                 5
  R2               4                 8
  RX               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"
D43V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0    20
  1Q LOSS WILD-TYPE     2                         1    56
D43V11, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  20                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"
D43V12, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    1  7
  1Q LOSS WILD-TYPE  7 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    7
  1Q LOSS WILD-TYPE    7   31
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               7                31
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED   14  2
  2P LOSS WILD-TYPE 43 31
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16                74 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                31 
$`2P LOSS MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JQ 
       30.31        57.53        99.88        69.37        49.22        36.26 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5KX TCGA-OR-A5LG 
       12.59        66.51        72.39        31.23        44.84        52.24 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       77.00        36.03        38.50        39.48 

$`2P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        44.45        18.12        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       17.79        76.64        16.11        67.59        18.48        39.25 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5JZ 
       15.25       121.25        29.82         9.50        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
      108.13        32.68       113.92        35.57        16.37        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ 
       95.18       153.63       127.50        68.25        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 
       58.55        60.89       152.15        31.79        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64         5.23        39.35        21.76        14.63 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       78.41        14.33        36.33        90.08        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG 
       79.07        61.05        28.04        18.05         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HC 
       20.25        22.32 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            12.59              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            99.88            153.63 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            47.03             34.70 
[1] "12.6 - 99.9 (47.0)" "0.0 - 153.6 (34.7)"
[1] "hr=" "3.8"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         1        8         3        3
  2P LOSS WILD-TYPE       8       35        15       15
D44V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                8                35
  STAGE III               3                15
  STAGE IV                3                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    1 10  2  2
  2P LOSS WILD-TYPE  8 38  9 18
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               1                 8
  T2              10                38
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   13  2
  2P LOSS WILD-TYPE 65  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     13    2
  2P LOSS WILD-TYPE   65    8
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              13                65
  1               2                 8
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    9  7
  2P LOSS WILD-TYPE 50 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    7
  2P LOSS WILD-TYPE   50   24
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               9                50
  MALE                 7                24
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   11  4
  2P LOSS WILD-TYPE 58 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     11    4
  2P LOSS WILD-TYPE   58   14
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               11                58
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  2P LOSS MUTATED                                       1
  2P LOSS WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  2P LOSS MUTATED                                          2
  2P LOSS WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  2P LOSS MUTATED                                     13
  2P LOSS WILD-TYPE                                   72
D44V8, multiclass
                                          clus
vv                                         2P LOSS MUTATED 2P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               2                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  13                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  2P LOSS MUTATED   11  1  1  1
  2P LOSS WILD-TYPE 52  6 11  4
D44V9, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              11                52
  R1               1                 6
  R2               1                11
  RX               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"
D44V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0    13
  2P LOSS WILD-TYPE     2                         1    63
D44V11, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  13                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"
D44V12, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    0  3
  2P LOSS WILD-TYPE  8 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    3
  2P LOSS WILD-TYPE    8   35
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               3                35
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED   12  2
  2Q LOSS WILD-TYPE 45 31
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14                76 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                31 
$`2Q LOSS MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JQ 
       30.31        57.53        99.88        69.37        49.22        36.26 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5LN TCGA-OR-A5LS 
       12.59        66.51        72.39        31.23        77.00        36.03 
TCGA-OU-A5PI TCGA-PK-A5HA 
       38.50        39.48 

$`2Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        44.45        18.12        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       17.79        76.64        16.11        67.59        18.48        39.25 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5JZ 
       15.25       121.25        29.82         9.50        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
      108.13        32.68       113.92        35.57        16.37        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        68.25        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       53.03        61.08        79.07        61.05        28.04        18.05 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
        0.00        24.85        20.25        22.32 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            12.59              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            99.88            153.63 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            44.35             35.95 
[1] "12.6 - 99.9 (44.3)" "0.0 - 153.6 (36.0)"
[1] "hr=" "3.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         1        8         1        3
  2Q LOSS WILD-TYPE       8       35        17       15
D45V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                8                35
  STAGE III               1                17
  STAGE IV                3                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2Q LOSS MUTATED    1  9  1  2
  2Q LOSS WILD-TYPE  8 39 10 18
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               1                 8
  T2               9                39
  T3               1                10
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   12  1
  2Q LOSS WILD-TYPE 66  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     12    1
  2Q LOSS WILD-TYPE   66    9
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              12                66
  1               1                 9
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    8  6
  2Q LOSS WILD-TYPE 51 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      8    6
  2Q LOSS WILD-TYPE   51   25
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               8                51
  MALE                 6                25
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    9  4
  2Q LOSS WILD-TYPE 60 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    4
  2Q LOSS WILD-TYPE   60   14
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                9                60
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  2Q LOSS MUTATED                                       1
  2Q LOSS WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  2Q LOSS MUTATED                                          2
  2Q LOSS WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  2Q LOSS MUTATED                                     11
  2Q LOSS WILD-TYPE                                   74
D45V8, multiclass
                                          clus
vv                                         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               2                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  11                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"
                   vv
clus                R0 R1 R2 RX
  2Q LOSS MUTATED   10  1  1  0
  2Q LOSS WILD-TYPE 53  6 11  5
D45V9, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              10                53
  R1               1                 6
  R2               1                11
  RX               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"
D45V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0    11
  2Q LOSS WILD-TYPE     2                         1    65
D45V11, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  11                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    0  1
  2Q LOSS WILD-TYPE  8 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    1
  2Q LOSS WILD-TYPE    8   37
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               1                37
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    9 10
  3P LOSS WILD-TYPE 48 23
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               19                71 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10                23 
$`3P LOSS MUTATED`
TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       91.30        42.51        16.11        30.31        18.12        57.53 
TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5JY 
       17.79        49.22        67.59        15.25        72.39        18.15 
TCGA-OR-A5K9 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM 
       11.31        28.31         5.23        14.33        53.03        61.08 
TCGA-OR-A5LS 
       36.03 

$`3P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        43.30        39.58        12.59        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       68.75        13.91        12.00        88.87        19.04        44.45 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       99.88        69.21        66.25        69.37        76.64        16.11 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       18.48        39.25        36.26       121.25        12.59        29.82 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
        9.50        66.51        31.23        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB 
      113.92        35.57        16.37        49.08        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       68.25        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD 
      152.15        31.79        29.10        28.64        23.64        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        52.24        78.41        36.33        90.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI 
       77.00        79.07        61.05        28.04        18.05        38.50 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
        0.00        24.85        20.25        39.48        22.32 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             5.23              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            91.30            153.63 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            30.31             39.35 
[1] "5.2 - 91.3 (30.3)"  "0.0 - 153.6 (39.4)"
[1] "hr=" "2"  
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         1        8         1        7
  3P LOSS WILD-TYPE       8       35        17       11
D46V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                8                35
  STAGE III               1                17
  STAGE IV                7                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    1  8  1  7
  3P LOSS WILD-TYPE  8 40 10 13
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               1                 8
  T2               8                40
  T3               1                10
  T4               7                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   15  2
  3P LOSS WILD-TYPE 63  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     15    2
  3P LOSS WILD-TYPE   63    8
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              15                63
  1               2                 8
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   10  9
  3P LOSS WILD-TYPE 49 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    9
  3P LOSS WILD-TYPE   49   22
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              10                49
  MALE                 9                22
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   12  4
  3P LOSS WILD-TYPE 57 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     12    4
  3P LOSS WILD-TYPE   57   14
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               12                57
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  3P LOSS MUTATED                                       0
  3P LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  3P LOSS MUTATED                                          0
  3P LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  3P LOSS MUTATED                                     19
  3P LOSS WILD-TYPE                                   66
D46V8, multiclass
                                          clus
vv                                         3P LOSS MUTATED 3P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  19                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED    9  4  4  0
  3P LOSS WILD-TYPE 54  3  8  5
D46V9, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               9                54
  R1               4                 3
  R2               4                 8
  RX               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"
D46V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         0    15
  3P LOSS WILD-TYPE     2                         1    61
D46V11, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  15                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    1  4
  3P LOSS WILD-TYPE  7 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    4
  3P LOSS WILD-TYPE    7   34
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               4                34
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    9 10
  3Q LOSS WILD-TYPE 48 23
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19                71 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10                23 
$`3Q LOSS MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA 
       33.83        91.30        42.51        88.87        16.11        30.31 
TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JW 
       57.53        17.79        49.22        67.59        15.25        72.39 
TCGA-OR-A5JY TCGA-OR-A5K9 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LL 
       18.15        11.31         5.23        21.76        14.33        53.03 
TCGA-OR-A5LM 
       61.08 

$`3Q LOSS WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        12.59        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD 
       13.91        12.00        19.04        44.45        18.12        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM 
       69.21        66.25        69.37        76.64        16.11        18.48 
TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       39.25        36.26       121.25        12.59        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       66.51        31.23        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
       35.57        16.37        49.08        24.62        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       44.84        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD 
       31.79        28.31        29.10        28.64        23.64        39.35 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN 
       14.63        52.24        78.41        36.33        90.08        77.00 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       79.07        61.05        28.04        36.03        18.05        38.50 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
        0.00        24.85        20.25        39.48        22.32 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             5.23              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            91.30            153.63 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            33.83             39.25 
[1] "5.2 - 91.3 (33.8)"  "0.0 - 153.6 (39.2)"
[1] "hr=" "1.8"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         1        9         1        6
  3Q LOSS WILD-TYPE       8       34        17       12
D47V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                9                34
  STAGE III               1                17
  STAGE IV                6                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q LOSS MUTATED    1  9  1  6
  3Q LOSS WILD-TYPE  8 39 10 14
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               1                 8
  T2               9                39
  T3               1                10
  T4               6                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   15  2
  3Q LOSS WILD-TYPE 63  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     15    2
  3Q LOSS WILD-TYPE   63    8
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              15                63
  1               2                 8
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   11  8
  3Q LOSS WILD-TYPE 48 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     11    8
  3Q LOSS WILD-TYPE   48   23
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              11                48
  MALE                 8                23
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   13  4
  3Q LOSS WILD-TYPE 56 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     13    4
  3Q LOSS WILD-TYPE   56   14
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               13                56
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  3Q LOSS MUTATED                                       0
  3Q LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  3Q LOSS MUTATED                                          0
  3Q LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  3Q LOSS MUTATED                                     19
  3Q LOSS WILD-TYPE                                   66
D47V8, multiclass
                                          clus
vv                                         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  19                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  3Q LOSS MUTATED   10  3  4  0
  3Q LOSS WILD-TYPE 53  4  8  5
D47V9, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              10                53
  R1               3                 4
  R2               4                 8
  RX               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"
D47V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         1    15
  3Q LOSS WILD-TYPE     2                         0    61
D47V11, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  15                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  4
  3Q LOSS WILD-TYPE  6 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    4
  3Q LOSS WILD-TYPE    6   34
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               4                34
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    2  7
  4P LOSS WILD-TYPE 55 26
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                81 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                7                26 
$`4P LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5KZ 
       18.12        18.48        12.59        18.15        32.68         4.11 
TCGA-OR-A5LC TCGA-OR-A5LI TCGA-PK-A5HA 
        5.23        14.33        39.48 

$`4P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        44.45        30.31        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       49.22        67.59        39.25        15.25        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
       29.82         9.50        66.51        72.39        31.23        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
      108.13       113.92        35.57        16.37        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 
      153.63       127.50        68.25        44.84        12.85        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       60.89       152.15        31.79        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       23.64        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       36.33        90.08        53.03        61.08        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       24.85        20.25        22.32 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             4.11              0.00 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            39.48            153.63 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            18.12             42.51 
[1] "4.1 - 39.5 (18.1)"  "0.0 - 153.6 (42.5)"
[1] "hr=" "6.3"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         1        2         1        5
  4P LOSS WILD-TYPE       8       41        17       13
D48V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                2                41
  STAGE III               1                17
  STAGE IV                5                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED    1  2  0  6
  4P LOSS WILD-TYPE  8 46 11 14
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               1                 8
  T2               2                46
  T3               0                11
  T4               6                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    8  1
  4P LOSS WILD-TYPE 70  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8    1
  4P LOSS WILD-TYPE   70    9
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               8                70
  1               1                 9
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    6  3
  4P LOSS WILD-TYPE 53 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6    3
  4P LOSS WILD-TYPE   53   28
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               6                53
  MALE                 3                28
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    4  4
  4P LOSS WILD-TYPE 65 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4    4
  4P LOSS WILD-TYPE   65   14
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                4                65
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  4P LOSS MUTATED                                       0
  4P LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  4P LOSS MUTATED                                          0
  4P LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  4P LOSS MUTATED                                      9
  4P LOSS WILD-TYPE                                   76
D48V8, multiclass
                                          clus
vv                                         4P LOSS MUTATED 4P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   9                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED    3  2  3  1
  4P LOSS WILD-TYPE 60  5  9  4
D48V9, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               3                60
  R1               2                 5
  R2               3                 9
  RX               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"
D48V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       0                         0     8
  4P LOSS WILD-TYPE     2                         1    68
D48V11, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   8                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"
D48V12, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    0  3
  4P LOSS WILD-TYPE  8 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0    3
  4P LOSS WILD-TYPE    8   35
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               3                35
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3  7
  4Q LOSS WILD-TYPE 54 26
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                80 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                26 
$`4Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5JY TCGA-OR-A5K2 
       16.11        18.12        18.48        12.59        18.15        32.68 
TCGA-OR-A5KO TCGA-OR-A5LC TCGA-OR-A5LI TCGA-PK-A5HA 
       46.49         5.23        14.33        39.48 

$`4Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        30.31        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       66.25        17.79        69.37        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       67.59        39.25        15.25        36.26       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
        9.50        66.51        72.39        31.23        27.02       108.13 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      113.92        35.57        16.37        49.08        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       68.25        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        28.31        29.10        28.64        23.64 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.35        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       90.08        53.03        61.08        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG 
       28.04        36.03        18.05        38.50         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HC 
       20.25        22.32 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             5.23              0.00 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            46.49            153.63 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           18.135            41.045 
[1] "5.2 - 46.5 (18.1)"  "0.0 - 153.6 (41.0)"
[1] "hr=" "4.5"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         1        1         2        6
  4Q LOSS WILD-TYPE       8       42        16       12
D49V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                1                42
  STAGE III               2                16
  STAGE IV                6                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED    1  1  1  7
  4Q LOSS WILD-TYPE  8 47 10 13
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               1                 8
  T2               1                47
  T3               1                10
  T4               7                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9  1
  4Q LOSS WILD-TYPE 69  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9    1
  4Q LOSS WILD-TYPE   69    9
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               9                69
  1               1                 9
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    8  2
  4Q LOSS WILD-TYPE 51 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8    2
  4Q LOSS WILD-TYPE   51   29
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               8                51
  MALE                 2                29
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    5  4
  4Q LOSS WILD-TYPE 64 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5    4
  4Q LOSS WILD-TYPE   64   14
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                5                64
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  4Q LOSS MUTATED                                       0
  4Q LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  4Q LOSS MUTATED                                          0
  4Q LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  4Q LOSS MUTATED                                     10
  4Q LOSS WILD-TYPE                                   75
D49V8, multiclass
                                          clus
vv                                         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  10                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"
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED    4  3  3  0
  4Q LOSS WILD-TYPE 59  4  9  5
D49V9, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0               4                59
  R1               3                 4
  R2               3                 9
  RX               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"
D49V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       0                         0     9
  4Q LOSS WILD-TYPE     2                         1    67
D49V11, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   9                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"
D49V12, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE  7 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE    7   35
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               3                35
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    3  4
  5P LOSS WILD-TYPE 54 29
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                83 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                29 
$`5P LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5JX TCGA-OR-A5KX TCGA-OR-A5LG TCGA-OR-A5LI 
       44.55        55.13        31.23        44.84        52.24        14.33 
TCGA-OR-A5LL 
       53.03 

$`5P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       44.45        30.31        18.12        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       66.25        17.79        69.37        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       67.59        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY 
       12.59        29.82         9.50        66.51        72.39        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.08        24.62        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY 
       83.80        95.18       153.63       127.50        68.25        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       14.63        78.41        36.33        90.08        61.08        77.00 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       79.07        61.05        28.04        36.03        18.05        38.50 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
        0.00        24.85        20.25        39.48        22.32 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            14.33              0.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            55.13            153.63 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            44.84             36.33 
[1] "14.3 - 55.1 (44.8)" "0.0 - 153.6 (36.3)"
[1] "hr=" "1.8"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0        2         3        2
  5P LOSS WILD-TYPE       9       41        15       16
D50V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II                2                41
  STAGE III               3                15
  STAGE IV                2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    0  3  3  1
  5P LOSS WILD-TYPE  9 45  8 19
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0                 9
  T2               3                45
  T3               3                 8
  T4               1                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    6  1
  5P LOSS WILD-TYPE 72  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    1
  5P LOSS WILD-TYPE   72    9
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6                72
  1               1                 9
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    4  3
  5P LOSS WILD-TYPE 55 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    3
  5P LOSS WILD-TYPE   55   28
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               4                55
  MALE                 3                28
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    6  1
  5P LOSS WILD-TYPE 63 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    1
  5P LOSS WILD-TYPE   63   17
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                6                63
  YES               1                17
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  5P LOSS MUTATED                                       0
  5P LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  5P LOSS MUTATED                                          0
  5P LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  5P LOSS MUTATED                                      7
  5P LOSS WILD-TYPE                                   78
D50V8, multiclass
                                          clus
vv                                         5P LOSS MUTATED 5P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   7                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"
                   vv
clus                R0 R1 R2 RX
  5P LOSS MUTATED    4  0  2  1
  5P LOSS WILD-TYPE 59  7 10  4
D50V9, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               4                59
  R1               0                 7
  R2               2                10
  RX               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"
D50V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     6
  5P LOSS WILD-TYPE     2                         1    70
D50V11, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   6                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"
D50V12, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  3
  5P LOSS WILD-TYPE  7 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    3
  5P LOSS WILD-TYPE    7   35
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               3                35
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    3  2
  5Q LOSS WILD-TYPE 54 31
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5                85 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                31 
$`5Q LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5JK TCGA-OR-A5KX TCGA-OR-A5LG TCGA-OR-A5LI 
       44.55        49.22        44.84        52.24        14.33 

$`5Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        30.31        18.12        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       67.59        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       16.37        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        29.10        28.64        23.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       21.76        14.63        78.41        36.33        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            14.33              0.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            52.24            153.63 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            44.84             36.33 
[1] "14.3 - 52.2 (44.8)" "0.0 - 153.6 (36.3)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         0        1         2        2
  5Q LOSS WILD-TYPE       9       42        16       16
D51V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II                1                42
  STAGE III               2                16
  STAGE IV                2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    0  2  1  2
  5Q LOSS WILD-TYPE  9 46 10 18
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0                 9
  T2               2                46
  T3               1                10
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    4  1
  5Q LOSS WILD-TYPE 74  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4    1
  5Q LOSS WILD-TYPE   74    9
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               4                74
  1               1                 9
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2  3
  5Q LOSS WILD-TYPE 57 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    3
  5Q LOSS WILD-TYPE   57   28
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               2                57
  MALE                 3                28
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    4  1
  5Q LOSS WILD-TYPE 65 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4    1
  5Q LOSS WILD-TYPE   65   17
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                4                65
  YES               1                17
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  5Q LOSS MUTATED                                       0
  5Q LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  5Q LOSS MUTATED                                          0
  5Q LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  5Q LOSS MUTATED                                      5
  5Q LOSS WILD-TYPE                                   80
D51V8, multiclass
                                          clus
vv                                         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   5                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"
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED    2  0  2  1
  5Q LOSS WILD-TYPE 61  7 10  4
D51V9, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               2                61
  R1               0                 7
  R2               2                10
  RX               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"
D51V10, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                30 
       TCGA-OR-A5KP        TCGA-P6-A5OG        TCGA-OR-A5J2        TCGA-OR-A5J3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-OR-A5J4        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-OR-A5JJ        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5KY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-OR-A5L9        TCGA-OR-A5LL        TCGA-OR-A5LM        TCGA-OR-A5LN 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-OR-A5LO        TCGA-OR-A5LP        TCGA-OR-A5LT        TCGA-OU-A5PI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-PK-A5HA        TCGA-PK-A5HC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         0     5
  5Q LOSS WILD-TYPE     2                         1    71
D51V11, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    0  3
  5Q LOSS WILD-TYPE  8 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    3
  5Q LOSS WILD-TYPE    8   35
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               3                35
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   10  9
  6P LOSS WILD-TYPE 47 24
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19                71 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9                24 
$`6P LOSS MUTATED`
TCGA-P6-A5OG TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JP 
       12.59        99.88        17.79        69.37        49.22        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5L2 
       36.26        12.59        66.51        18.15        32.68        60.89 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT 
        5.23        21.76        14.33        53.03        36.03        18.05 
TCGA-OU-A5PI 
       38.50 

$`6P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE 
       19.04        44.45        30.31        18.12        57.53        69.21 
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       66.25        76.64        16.11        67.59        18.48        39.25 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
      121.25        29.82         9.50        72.39        31.23        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
      108.13       113.92        35.57        16.37        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        68.25        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55       152.15        31.79        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       23.64        39.35        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        61.08        77.00        79.07        61.05        28.04 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
        0.00        24.85        20.25        39.48        22.32 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             5.23              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            99.88            153.63 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            32.68             39.58 
[1] "5.2 - 99.9 (32.7)"  "0.0 - 153.6 (39.6)"
[1] "hr=" "1.9"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         0       10         2        7
  6P LOSS WILD-TYPE       9       33        16       11
D52V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II               10                33
  STAGE III               2                16
  STAGE IV                7                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    0 11  1  7
  6P LOSS WILD-TYPE  9 37 10 13
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               0                 9
  T2              11                37
  T3               1                10
  T4               7                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   16  3
  6P LOSS WILD-TYPE 62  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     16    3
  6P LOSS WILD-TYPE   62    7
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              16                62
  1               3                 7
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   13  6
  6P LOSS WILD-TYPE 46 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     13    6
  6P LOSS WILD-TYPE   46   25
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              13                46
  MALE                 6                25
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   14  4
  6P LOSS WILD-TYPE 55 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14    4
  6P LOSS WILD-TYPE   55   14
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               14                55
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  6P LOSS MUTATED                                       1
  6P LOSS WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  6P LOSS MUTATED                                          2
  6P LOSS WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  6P LOSS MUTATED                                     16
  6P LOSS WILD-TYPE                                   69
D52V8, multiclass
                                          clus
vv                                         6P LOSS MUTATED 6P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               2                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  16                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"
                   vv
clus                R0 R1 R2 RX
  6P LOSS MUTATED   12  1  5  0
  6P LOSS WILD-TYPE 51  6  7  5
D52V9, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              12                51
  R1               1                 6
  R2               5                 7
  RX               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"
D52V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       0                         0    16
  6P LOSS WILD-TYPE     2                         1    60
D52V11, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16                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"
D52V12, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    0  6
  6P LOSS WILD-TYPE  8 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    6
  6P LOSS WILD-TYPE    8   32
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               6                32
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   11 11
  6Q LOSS WILD-TYPE 46 22
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                68 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               11                22 
$`6Q LOSS MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       12.59        16.11        18.12        99.88        17.79        69.37 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY 
       49.22        15.25        36.26        12.59        66.51        18.15 
TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5L2 TCGA-OR-A5LC TCGA-OR-A5LI TCGA-OR-A5LL 
       32.68        46.49        60.89         5.23        14.33        53.03 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       36.03        18.05        38.50         0.00 

$`6Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       55.13        68.75        13.91        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI 
       44.45        30.31        57.53        69.21        66.25        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JT 
       16.11        67.59        18.48        39.25       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
        9.50        72.39        31.23        27.02       108.13       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       35.57        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84        12.85         4.11        58.55       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE 
       28.31        29.10        28.64        23.64        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
       14.63        52.24        78.41        36.33        90.08        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5H9 
       77.00        79.07        61.05        28.04        24.85        20.25 
TCGA-PK-A5HA TCGA-PK-A5HC 
       39.48        22.32 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.00              4.11 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            99.88            153.63 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           25.415            41.045 
[1] "0.0 - 99.9 (25.4)"  "4.1 - 153.6 (41.0)"
[1] "hr=" "2.3"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         0        9         3       10
  6Q LOSS WILD-TYPE       9       34        15        8
D53V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II                9                34
  STAGE III               3                15
  STAGE IV               10                 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"
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    0 10  2 10
  6Q LOSS WILD-TYPE  9 38  9 10
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               0                 9
  T2              10                38
  T3               2                 9
  T4              10                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   19  3
  6Q LOSS WILD-TYPE 59  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     19    3
  6Q LOSS WILD-TYPE   59    7
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              19                59
  1               3                 7
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   16  6
  6Q LOSS WILD-TYPE 43 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     16    6
  6Q LOSS WILD-TYPE   43   25
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              16                43
  MALE                 6                25
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   16  4
  6Q LOSS WILD-TYPE 53 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     16    4
  6Q LOSS WILD-TYPE   53   14
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               16                53
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  6Q LOSS MUTATED                                       1
  6Q LOSS WILD-TYPE                                     0
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  6Q LOSS MUTATED                                          2
  6Q LOSS WILD-TYPE                                        2
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  6Q LOSS MUTATED                                     19
  6Q LOSS WILD-TYPE                                   66
D53V8, multiclass
                                          clus
vv                                         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  1                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               2                 2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  19                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED   12  3  6  0
  6Q LOSS WILD-TYPE 51  4  6  5
D53V9, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              12                51
  R1               3                 4
  R2               6                 6
  RX               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"
D53V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       0                         0    19
  6Q LOSS WILD-TYPE     2                         1    57
D53V11, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  19                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"
D53V12, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    1  7
  6Q LOSS WILD-TYPE  7 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    7
  6Q LOSS WILD-TYPE    7   31
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               7                31
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    2  3
  7P LOSS WILD-TYPE 55 30
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                85 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                30 
$`7P LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JP TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LT 
       57.53        15.25        39.35        14.33        18.05 

$`7P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       16.11        19.04        44.45        30.31        18.12        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       49.22        67.59        18.48        39.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       16.37        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       44.84        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        52.24        78.41        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       36.03        38.50         0.00        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            14.33              0.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            57.53            153.63 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            18.05             39.25 
[1] "14.3 - 57.5 (18.1)" "0.0 - 153.6 (39.2)"
[1] "hr=" "2.6"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED         0        1         2        1
  7P LOSS WILD-TYPE       9       42        16       17
D54V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II                1                42
  STAGE III               2                16
  STAGE IV                1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7P LOSS MUTATED    0  1  1  2
  7P LOSS WILD-TYPE  9 47 10 18
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               0                 9
  T2               1                47
  T3               1                10
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    4  0
  7P LOSS WILD-TYPE 74 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4    0
  7P LOSS WILD-TYPE   74   10
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               4                74
  1               0                10
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    1  4
  7P LOSS WILD-TYPE 58 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    4
  7P LOSS WILD-TYPE   58   27
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               1                58
  MALE                 4                27
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    4  0
  7P LOSS WILD-TYPE 65 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4    0
  7P LOSS WILD-TYPE   65   18
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                4                65
  YES               0                18
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  7P LOSS MUTATED                                       0
  7P LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  7P LOSS MUTATED                                          0
  7P LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  7P LOSS MUTATED                                      5
  7P LOSS WILD-TYPE                                   80
D54V8, multiclass
                                          clus
vv                                         7P LOSS MUTATED 7P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   5                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"
                   vv
clus                R0 R1 R2 RX
  7P LOSS MUTATED    2  0  1  1
  7P LOSS WILD-TYPE 61  7 11  4
D54V9, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               2                61
  R1               0                 7
  R2               1                11
  RX               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"
D54V10, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                30 
       TCGA-OR-A5KP        TCGA-P6-A5OG        TCGA-OR-A5J2        TCGA-OR-A5J3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-OR-A5J4        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JG 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-OR-A5JJ        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5K5        TCGA-OR-A5KB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-OR-A5KU        TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5KY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-OR-A5L9        TCGA-OR-A5LG        TCGA-OR-A5LL        TCGA-OR-A5LM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-OR-A5LN        TCGA-OR-A5LO        TCGA-OR-A5LP        TCGA-OU-A5PI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-PK-A5HA        TCGA-PK-A5HC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       0                         0     4
  7P LOSS WILD-TYPE     2                         1    72
D54V11, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    0  2
  7P LOSS WILD-TYPE  8 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE    8   36
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               2                36
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    1  5
  7Q LOSS WILD-TYPE 56 28
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                84 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5                28 
$`7Q LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5K5 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LT 
       57.53        69.21        16.37        39.35        14.33        18.05 

$`7Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       16.11        19.04        44.45        30.31        18.12        99.88 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       66.25        17.79        69.37        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       67.59        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.08        24.62        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LE 
       28.31        29.10        28.64        23.64         5.23        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50         0.00        24.85        20.25        39.48        22.32 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            14.33              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            69.21            153.63 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           28.700            38.875 
[1] "14.3 - 69.2 (28.7)" "0.0 - 153.6 (38.9)"
[1] "hr=" "3"  
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         1        0         3        1
  7Q LOSS WILD-TYPE       8       43        15       17
D55V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                0                43
  STAGE III               3                15
  STAGE IV                1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7Q LOSS MUTATED    1  0  2  2
  7Q LOSS WILD-TYPE  8 48  9 18
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               1                 8
  T2               0                48
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V5, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    5  0
  7Q LOSS WILD-TYPE 73 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      5    0
  7Q LOSS WILD-TYPE   73   10
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               5                73
  1               0                10
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    3  3
  7Q LOSS WILD-TYPE 56 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    3
  7Q LOSS WILD-TYPE   56   28
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                56
  MALE                 3                28
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    4  1
  7Q LOSS WILD-TYPE 65 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    1
  7Q LOSS WILD-TYPE   65   17
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                4                65
  YES               1                17
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  7Q LOSS MUTATED                                       0
  7Q LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  7Q LOSS MUTATED                                          0
  7Q LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  7Q LOSS MUTATED                                      6
  7Q LOSS WILD-TYPE                                   79
D55V8, multiclass
                                          clus
vv                                         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   6                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"
                   vv
clus                R0 R1 R2 RX
  7Q LOSS MUTATED    3  0  1  1
  7Q LOSS WILD-TYPE 60  7 11  4
D55V9, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               3                60
  R1               0                 7
  R2               1                11
  RX               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"
D55V10, continuous
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                29 
       TCGA-OR-A5KP        TCGA-P6-A5OG        TCGA-OR-A5J2        TCGA-OR-A5J3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-OR-A5J4        TCGA-OR-A5J7        TCGA-OR-A5J8        TCGA-OR-A5JG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-OR-A5JJ        TCGA-OR-A5JT        TCGA-OR-A5JV        TCGA-OR-A5JX 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-OR-A5JY        TCGA-OR-A5K2        TCGA-OR-A5KB        TCGA-OR-A5KU 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-OR-A5KV        TCGA-OR-A5KW        TCGA-OR-A5KY        TCGA-OR-A5L9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-OR-A5LG        TCGA-OR-A5LL        TCGA-OR-A5LM        TCGA-OR-A5LN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-OR-A5LO        TCGA-OR-A5LP        TCGA-OU-A5PI        TCGA-PK-A5HA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-PK-A5HC 
"7Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         0     5
  7Q LOSS WILD-TYPE     2                         1    71
D55V11, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    0  2
  7Q LOSS WILD-TYPE  8 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    2
  7Q LOSS WILD-TYPE    8   36
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               2                36
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   10  6
  8P LOSS WILD-TYPE 47 27
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                74 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6                27 
$`8P LOSS MUTATED`
TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JG 
       91.30        42.51        16.11        30.31        18.12        17.79 
TCGA-OR-A5JL TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5KX TCGA-OR-A5LG 
       67.59        72.39        49.08        24.36        44.84        52.24 
TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OU-A5PI 
       14.33        53.03        36.03        38.50 

$`8P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        43.30        39.58        12.59        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       68.75        13.91        12.00        88.87        19.04        44.45 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       57.53        99.88        69.21        66.25        69.37        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       16.11        49.22        18.48        39.25        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX 
      121.25        12.59        29.82         9.50        66.51        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       16.37        24.62        11.31        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ 
       95.18       153.63       127.50        68.25        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 
       58.55        60.89       152.15        31.79        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64         5.23        39.35        21.76        14.63 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        36.33        90.08        61.08        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       61.05        28.04        18.05         0.00        24.85        20.25 
TCGA-PK-A5HA TCGA-PK-A5HC 
       39.48        22.32 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            14.33              0.00 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            91.30            153.63 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           40.505            37.790 
[1] "14.3 - 91.3 (40.5)" "0.0 - 153.6 (37.8)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         1        6         3        5
  8P LOSS WILD-TYPE       8       37        15       13
D56V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                6                37
  STAGE III               3                15
  STAGE IV                5                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED    1  8  2  4
  8P LOSS WILD-TYPE  8 40  9 16
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               1                 8
  T2               8                40
  T3               2                 9
  T4               4                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   12  3
  8P LOSS WILD-TYPE 66  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     12    3
  8P LOSS WILD-TYPE   66    7
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              12                66
  1               3                 7
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   11  5
  8P LOSS WILD-TYPE 48 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11    5
  8P LOSS WILD-TYPE   48   26
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              11                48
  MALE                 5                26
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   12  2
  8P LOSS WILD-TYPE 57 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     12    2
  8P LOSS WILD-TYPE   57   16
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               12                57
  YES               2                16
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  8P LOSS MUTATED                                       0
  8P LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  8P LOSS MUTATED                                          0
  8P LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  8P LOSS MUTATED                                     16
  8P LOSS WILD-TYPE                                   69
D56V8, multiclass
                                          clus
vv                                         8P LOSS MUTATED 8P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  16                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"
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED    8  4  1  1
  8P LOSS WILD-TYPE 55  3 11  4
D56V9, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0               8                55
  R1               4                 3
  R2               1                11
  RX               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"
D56V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       0                         0    13
  8P LOSS WILD-TYPE     2                         1    63
D56V11, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  13                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"
D56V12, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  7
  8P LOSS WILD-TYPE  7 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    7
  8P LOSS WILD-TYPE    7   31
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               7                31
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    8  4
  8Q LOSS WILD-TYPE 49 29
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12                78 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                29 
$`8Q LOSS MUTATED`
TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JG TCGA-OR-A5JL 
       91.30        42.51        16.11        30.31        17.79        67.59 
TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5KX TCGA-OR-A5LI TCGA-OR-A5LS TCGA-OU-A5PI 
       72.39        49.08        44.84        14.33        36.03        38.50 

$`8Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        43.30        39.58        12.59        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       68.75        13.91        12.00        88.87        19.04        44.45 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH 
       18.12        57.53        99.88        69.21        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       76.64        16.11        49.22        18.48        39.25        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       35.57        16.37        24.62        11.31        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        29.10        28.64        23.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        52.24        78.41        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       18.05         0.00        24.85        20.25        39.48        22.32 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            14.33              0.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            91.30            153.63 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           40.505            37.790 
[1] "14.3 - 91.3 (40.5)" "0.0 - 153.6 (37.8)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         1        4         2        4
  8Q LOSS WILD-TYPE       8       39        16       14
D57V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                4                39
  STAGE III               2                16
  STAGE IV                4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q LOSS MUTATED    1  6  1  3
  8Q LOSS WILD-TYPE  8 42 10 17
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1                 8
  T2               6                42
  T3               1                10
  T4               3                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    8  3
  8Q LOSS WILD-TYPE 70  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      8    3
  8Q LOSS WILD-TYPE   70    7
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               8                70
  1               3                 7
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    9  3
  8Q LOSS WILD-TYPE 50 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9    3
  8Q LOSS WILD-TYPE   50   28
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               9                50
  MALE                 3                28
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    9  2
  8Q LOSS WILD-TYPE 60 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9    2
  8Q LOSS WILD-TYPE   60   16
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                9                60
  YES               2                16
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  8Q LOSS MUTATED                                       0
  8Q LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  8Q LOSS MUTATED                                          0
  8Q LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  8Q LOSS MUTATED                                     12
  8Q LOSS WILD-TYPE                                   73
D57V8, multiclass
                                          clus
vv                                         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  12                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  8Q LOSS MUTATED    6  3  1  0
  8Q LOSS WILD-TYPE 57  4 11  5
D57V9, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               6                57
  R1               3                 4
  R2               1                11
  RX               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"
D57V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         0    10
  8Q LOSS WILD-TYPE     2                         1    66
D57V11, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  10                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  5
  8Q LOSS WILD-TYPE  7 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    5
  8Q LOSS WILD-TYPE    7   33
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               5                33
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   11  9
  9P LOSS WILD-TYPE 46 24
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20                70 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                24 
$`9P LOSS MUTATED`
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JK 
       33.83        12.59        19.04        44.45        57.53        49.22 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 
       18.48        15.25        12.59        66.51        18.15        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LE 
       16.37        49.08        24.36       152.15         5.23        21.76 
TCGA-OR-A5LG TCGA-OR-A5LM 
       52.24        61.08 

$`9P LOSS WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA 
       68.75        13.91        12.00        88.87        16.11        30.31 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       18.12        99.88        69.21        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        16.11        67.59        39.25        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       29.82         9.50        72.39        31.23        27.02       108.13 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KQ 
      113.92        35.57        24.62        11.31        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 
       12.85         4.11        58.55        60.89        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH 
       29.10        28.64        23.64        39.35        14.63        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO 
       14.33        36.33        90.08        53.03        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        20.25        39.48        22.32 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             5.23              0.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           152.15            153.63 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           28.520            39.415 
[1] "5.2 - 152.2 (28.5)" "0.0 - 153.6 (39.4)"
[1] "hr=" "1.7"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         1        9         4        5
  9P LOSS WILD-TYPE       8       34        14       13
D58V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                9                34
  STAGE III               4                14
  STAGE IV                5                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED    1  9  3  6
  9P LOSS WILD-TYPE  8 39  8 14
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               1                 8
  T2               9                39
  T3               3                 8
  T4               6                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   18  1
  9P LOSS WILD-TYPE 60  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     18    1
  9P LOSS WILD-TYPE   60    9
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              18                60
  1               1                 9
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   12  8
  9P LOSS WILD-TYPE 47 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12    8
  9P LOSS WILD-TYPE   47   23
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              12                47
  MALE                 8                23
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   12  7
  9P LOSS WILD-TYPE 57 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12    7
  9P LOSS WILD-TYPE   57   11
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               12                57
  YES               7                11
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  9P LOSS MUTATED                                       0
  9P LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  9P LOSS MUTATED                                          0
  9P LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  9P LOSS MUTATED                                     20
  9P LOSS WILD-TYPE                                   65
D58V8, multiclass
                                          clus
vv                                         9P LOSS MUTATED 9P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  20                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED   13  1  4  1
  9P LOSS WILD-TYPE 50  6  8  4
D58V9, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              13                50
  R1               1                 6
  R2               4                 8
  RX               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"
D58V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       0                         0    19
  9P LOSS WILD-TYPE     2                         1    57
D58V11, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  19                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"
D58V12, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    2  7
  9P LOSS WILD-TYPE  6 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2    7
  9P LOSS WILD-TYPE    6   31
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               7                31
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    8  4
  9Q LOSS WILD-TYPE 49 29
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12                78 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                29 
$`9Q LOSS MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JS 
       12.59        44.45        57.53        49.22        18.48        12.59 
TCGA-OR-A5JV TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LM 
       66.51        49.08        24.36       152.15         5.23        61.08 

$`9Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        30.31        18.12        99.88        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO 
       17.79        69.37        76.64        16.11        67.59        39.25 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       15.25        36.26       121.25        29.82         9.50        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KQ 
       35.57        16.37        24.62        11.31        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 
       12.85         4.11        58.55        60.89        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       29.10        28.64        23.64        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        36.33        90.08        53.03 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       77.00        79.07        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50         0.00        24.85        20.25        39.48        22.32 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             5.23              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           152.15            153.63 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           46.765            37.415 
[1] "5.2 - 152.2 (46.8)" "0.0 - 153.6 (37.4)"
[1] "hr=" "1"  
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         1        6         0        4
  9Q LOSS WILD-TYPE       8       37        18       14
D59V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                6                37
  STAGE III               0                18
  STAGE IV                4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED    1  6  0  4
  9Q LOSS WILD-TYPE  8 42 11 16
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               1                 8
  T2               6                42
  T3               0                11
  T4               4                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   11  0
  9Q LOSS WILD-TYPE 67 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     11    0
  9Q LOSS WILD-TYPE   67   10
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              11                67
  1               0                10
[1] 2 2
[1] FALSE
D59V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    8  4
  9Q LOSS WILD-TYPE 51 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8    4
  9Q LOSS WILD-TYPE   51   27
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               8                51
  MALE                 4                27
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    8  3
  9Q LOSS WILD-TYPE 61 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8    3
  9Q LOSS WILD-TYPE   61   15
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                8                61
  YES               3                15
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  9Q LOSS MUTATED                                       0
  9Q LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  9Q LOSS MUTATED                                          0
  9Q LOSS WILD-TYPE                                        4
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  9Q LOSS MUTATED                                     12
  9Q LOSS WILD-TYPE                                   73
D59V8, multiclass
                                          clus
vv                                         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               0                 4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  12                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED    7  1  3  0
  9Q LOSS WILD-TYPE 56  6  9  5
D59V9, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0               7                56
  R1               1                 6
  R2               3                 9
  RX               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"
D59V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         0    11
  9Q LOSS WILD-TYPE     2                         1    65
D59V11, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  11                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    1  5
  9Q LOSS WILD-TYPE  7 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1    5
  9Q LOSS WILD-TYPE    7   33
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               5                33
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    6  6
  10P LOSS WILD-TYPE 51 27
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                 78 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 27 
$`10P LOSS MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JQ 
       13.91        30.31        69.21        17.79        69.37        36.26 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LM 
       12.59        66.51        18.15        60.89        28.31        61.08 

$`10P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        68.75        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        44.45        18.12        57.53        99.88        66.25 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       76.64        16.11        49.22        67.59        18.48        39.25 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX 
       15.25       121.25        29.82         9.50        72.39        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.08        24.62        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 
       12.85         4.11        58.55       152.15        31.79        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        36.33        90.08        53.03 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       77.00        79.07        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50         0.00        24.85        20.25        39.48        22.32 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             12.59               0.00 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             69.37             153.63 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            33.285             39.300 
[1] "12.6 - 69.4 (33.3)" "0.0 - 153.6 (39.3)"
[1] "hr=" "1.6"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         1        7         0        4
  10P LOSS WILD-TYPE       8       36        18       14
D60V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 7                 36
  STAGE III                0                 18
  STAGE IV                 4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    1  7  1  3
  10P LOSS WILD-TYPE  8 41 10 17
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                1                  8
  T2                7                 41
  T3                1                 10
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    9  3
  10P LOSS WILD-TYPE 69  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9    3
  10P LOSS WILD-TYPE   69    7
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                9                 69
  1                3                  7
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    8  4
  10P LOSS WILD-TYPE 51 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8    4
  10P LOSS WILD-TYPE   51   27
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                8                 51
  MALE                  4                 27
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    9  2
  10P LOSS WILD-TYPE 60 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9    2
  10P LOSS WILD-TYPE   60   16
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 9                 60
  YES                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  10P LOSS MUTATED                                       1
  10P LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  10P LOSS MUTATED                                          1
  10P LOSS WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  10P LOSS MUTATED                                     10
  10P LOSS WILD-TYPE                                   75
D60V8, multiclass
                                          clus
vv                                         10P LOSS MUTATED 10P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                1                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   10                 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"
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED    8  2  2  0
  10P LOSS WILD-TYPE 55  5 10  5
D60V9, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                8                 55
  R1                2                  5
  R2                2                 10
  RX                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"
D60V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         0    11
  10P LOSS WILD-TYPE     2                         1    65
D60V11, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   11                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  2
  10P LOSS WILD-TYPE  7 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    2
  10P LOSS WILD-TYPE    7   36
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 36
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    5  5
  10Q LOSS WILD-TYPE 52 28
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 80 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 28 
$`10Q LOSS MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5JS 
       30.31        69.21        17.79        69.37        36.26        12.59 
TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5L2 TCGA-OR-A5L6 
       66.51        18.15        60.89        28.31 

$`10Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        44.45        18.12        57.53        99.88 
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM 
       66.25        76.64        16.11        49.22        67.59        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       39.25        15.25       121.25        29.82         9.50        72.39 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       31.23        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       16.37        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84        12.85         4.11        58.55       152.15        31.79 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        38.50         0.00        24.85        20.25 
TCGA-PK-A5HA TCGA-PK-A5HC 
       39.48        22.32 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             12.59               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             69.37             153.63 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            33.285             39.300 
[1] "12.6 - 69.4 (33.3)" "0.0 - 153.6 (39.3)"
[1] "hr=" "1.5"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         1        6         0        3
  10Q LOSS WILD-TYPE       8       37        18       15
D61V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 6                 37
  STAGE III                0                 18
  STAGE IV                 3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    1  6  0  3
  10Q LOSS WILD-TYPE  8 42 11 17
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                1                  8
  T2                6                 42
  T3                0                 11
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    8  2
  10Q LOSS WILD-TYPE 70  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      8    2
  10Q LOSS WILD-TYPE   70    8
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                8                 70
  1                2                  8
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    7  3
  10Q LOSS WILD-TYPE 52 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7    3
  10Q LOSS WILD-TYPE   52   28
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                7                 52
  MALE                  3                 28
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    7  2
  10Q LOSS WILD-TYPE 62 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7    2
  10Q LOSS WILD-TYPE   62   16
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 7                 62
  YES                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  10Q LOSS MUTATED                                       1
  10Q LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  10Q LOSS MUTATED                                          1
  10Q LOSS WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  10Q LOSS MUTATED                                      8
  10Q LOSS WILD-TYPE                                   77
D61V8, multiclass
                                          clus
vv                                         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                1                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    8                 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"
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED    7  2  1  0
  10Q LOSS WILD-TYPE 56  5 11  5
D61V9, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                7                 56
  R1                2                  5
  R2                1                 11
  RX                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"
D61V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         0    10
  10Q LOSS WILD-TYPE     2                         1    66
D61V11, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   10                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    0  2
  10Q LOSS WILD-TYPE  8 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0    2
  10Q LOSS WILD-TYPE    8   36
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 36
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   16  7
  11P LOSS WILD-TYPE 41 26
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                23                 67 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 26 
$`11P LOSS MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG 
       42.51        16.11        30.31        57.53        99.88        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW 
       69.37        76.64        49.22        36.26        66.51        72.39 
TCGA-OR-A5JY TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5L6 TCGA-OR-A5LC 
       18.15        49.08        11.31        24.36        28.31         5.23 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       61.08        77.00        36.03        38.50        39.48 

$`11P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        12.59        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       55.13        68.75        13.91        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       44.45        18.12        69.21        66.25        16.11        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       18.48        39.25        15.25       121.25        12.59        29.82 
TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
        9.50        31.23        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       35.57        16.37        24.62        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        68.25        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 
        4.11        58.55        60.89       152.15        31.79        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       28.64        23.64        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
       78.41        14.33        36.33        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       61.05        28.04        18.05         0.00        24.85        20.25 
TCGA-PK-A5HC 
       22.32 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              5.23               0.00 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             99.88             153.63 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             39.48              36.33 
[1] "5.2 - 99.9 (39.5)"  "0.0 - 153.6 (36.3)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         2       12         1        6
  11P LOSS WILD-TYPE       7       31        17       12
D62V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  2                  7
  STAGE II                12                 31
  STAGE III                1                 17
  STAGE IV                 6                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    2 13  1  5
  11P LOSS WILD-TYPE  7 35 10 15
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                  7
  T2               13                 35
  T3                1                 10
  T4                5                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   18  3
  11P LOSS WILD-TYPE 60  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18    3
  11P LOSS WILD-TYPE   60    7
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               18                 60
  1                3                  7
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   13 10
  11P LOSS WILD-TYPE 46 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13   10
  11P LOSS WILD-TYPE   46   21
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               13                 46
  MALE                 10                 21
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   17  4
  11P LOSS WILD-TYPE 52 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     17    4
  11P LOSS WILD-TYPE   52   14
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                17                 52
  YES                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  11P LOSS MUTATED                                       1
  11P LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  11P LOSS MUTATED                                          2
  11P LOSS WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  11P LOSS MUTATED                                     20
  11P LOSS WILD-TYPE                                   65
D62V8, multiclass
                                          clus
vv                                         11P LOSS MUTATED 11P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   20                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  11P LOSS MUTATED   14  3  3  0
  11P LOSS WILD-TYPE 49  4  9  5
D62V9, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               14                 49
  R1                3                  4
  R2                3                  9
  RX                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"
D62V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       0                         0    18
  11P LOSS WILD-TYPE     2                         1    58
D62V11, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   18                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    1  5
  11P LOSS WILD-TYPE  7 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    5
  11P LOSS WILD-TYPE    7   33
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                5                 33
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   17  5
  11Q LOSS WILD-TYPE 40 28
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 68 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 28 
$`11Q LOSS MUTATED`
TCGA-PK-A5HB TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       42.51        30.31        57.53        99.88        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW 
       76.64        49.22        36.26        12.59        66.51        72.39 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LM 
       49.08        11.31        24.36        28.31         5.23        61.08 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       77.00        36.03        38.50        39.48 

$`11Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        12.59        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       19.04        44.45        18.12        69.21        66.25        16.11 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       67.59        18.48        39.25        15.25       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
        9.50        31.23        18.15        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ 
      113.92        35.57        16.37        24.62        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       29.10        28.64        23.64        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        36.33        90.08        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG 
       79.07        61.05        28.04        18.05         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HC 
       20.25        22.32 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              5.23               0.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             99.88             153.63 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            40.995             35.950 
[1] "5.2 - 99.9 (41.0)"  "0.0 - 153.6 (36.0)"
[1] "hr=" "1.8"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         2       13         0        5
  11Q LOSS WILD-TYPE       7       30        18       13
D63V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  2                  7
  STAGE II                13                 30
  STAGE III                0                 18
  STAGE IV                 5                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    2 14  0  4
  11Q LOSS WILD-TYPE  7 34 11 16
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                2                  7
  T2               14                 34
  T3                0                 11
  T4                4                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   18  2
  11Q LOSS WILD-TYPE 60  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     18    2
  11Q LOSS WILD-TYPE   60    8
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               18                 60
  1                2                  8
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   12 10
  11Q LOSS WILD-TYPE 47 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     12   10
  11Q LOSS WILD-TYPE   47   21
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               12                 47
  MALE                 10                 21
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   16  4
  11Q LOSS WILD-TYPE 53 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     16    4
  11Q LOSS WILD-TYPE   53   14
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                16                 53
  YES                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  11Q LOSS MUTATED                                       1
  11Q LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  11Q LOSS MUTATED                                          2
  11Q LOSS WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  11Q LOSS MUTATED                                     19
  11Q LOSS WILD-TYPE                                   66
D63V8, multiclass
                                          clus
vv                                         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   19                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED   15  2  2  0
  11Q LOSS WILD-TYPE 48  5 10  5
D63V9, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               15                 48
  R1                2                  5
  R2                2                 10
  RX                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"
D63V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       0                         0    17
  11Q LOSS WILD-TYPE     2                         1    59
D63V11, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   17                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  5
  11Q LOSS WILD-TYPE  8 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    5
  11Q LOSS WILD-TYPE    8   33
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                5                 33
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    2  3
  12P LOSS WILD-TYPE 55 30
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 85 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 30 
$`12P LOSS MUTATED`
TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5JB TCGA-OR-A5LG TCGA-OR-A5LL 
       12.59        42.51        18.12        52.24        53.03 

$`12P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        91.30        43.30        39.58        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       44.45        30.31        57.53        99.88        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        69.37        76.64        16.11        49.22        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       18.48        39.25        15.25        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.08        24.62        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        29.10        28.64        23.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        78.41        14.33        36.33        90.08 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             12.59               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             53.03             153.63 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             42.51              38.50 
[1] "12.6 - 53.0 (42.5)" "0.0 - 153.6 (38.5)"
[1] "hr=" "2.2"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         0        1         1        2
  12P LOSS WILD-TYPE       9       42        17       16
D64V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                1                 17
  STAGE IV                 2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    0  1  1  2
  12P LOSS WILD-TYPE  9 47 10 18
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                1                 10
  T4                2                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    4  0
  12P LOSS WILD-TYPE 74 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    0
  12P LOSS WILD-TYPE   74   10
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                4                 74
  1                0                 10
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  3
  12P LOSS WILD-TYPE 57 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    3
  12P LOSS WILD-TYPE   57   28
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  3                 28
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    3  1
  12P LOSS WILD-TYPE 66 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    1
  12P LOSS WILD-TYPE   66   17
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 3                 66
  YES                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  12P LOSS MUTATED                                       0
  12P LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  12P LOSS MUTATED                                          0
  12P LOSS WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  12P LOSS MUTATED                                      5
  12P LOSS WILD-TYPE                                   80
D64V8, multiclass
                                          clus
vv                                         12P LOSS MUTATED 12P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    5                 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"
                    vv
clus                 R0 R1 R2 RX
  12P LOSS MUTATED    1  1  1  1
  12P LOSS WILD-TYPE 62  6 11  4
D64V9, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0                1                 62
  R1                1                  6
  R2                1                 11
  RX                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"
D64V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0     3
  12P LOSS WILD-TYPE     2                         1    73
D64V11, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    0  2
  12P LOSS WILD-TYPE  8 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    2
  12P LOSS WILD-TYPE    8   36
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 36
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    1  3
  12Q LOSS WILD-TYPE 56 30
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 86 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 30 
$`12Q LOSS MUTATED`
TCGA-P6-A5OG TCGA-OR-A5JB TCGA-OR-A5LG TCGA-OR-A5LL 
       12.59        18.12        52.24        53.03 

$`12Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        30.31        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       66.25        17.79        69.37        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       67.59        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       16.37        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       44.84        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       39.35        21.76        14.63        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        38.50         0.00        24.85        20.25 
TCGA-PK-A5HA TCGA-PK-A5HC 
       39.48        22.32 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             12.59               0.00 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             53.03             153.63 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            35.180             38.875 
[1] "12.6 - 53.0 (35.2)" "0.0 - 153.6 (38.9)"
[1] "hr=" "3"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         0        1         1        2
  12Q LOSS WILD-TYPE       9       42        17       16
D65V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                1                 17
  STAGE IV                 2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    0  1  1  2
  12Q LOSS WILD-TYPE  9 47 10 18
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                1                 10
  T4                2                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    4  0
  12Q LOSS WILD-TYPE 74 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4    0
  12Q LOSS WILD-TYPE   74   10
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                4                 74
  1                0                 10
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  2
  12Q LOSS WILD-TYPE 57 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    2
  12Q LOSS WILD-TYPE   57   29
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  2                 29
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  0
  12Q LOSS WILD-TYPE 66 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    0
  12Q LOSS WILD-TYPE   66   18
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 3                 66
  YES                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  12Q LOSS MUTATED                                       0
  12Q LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  12Q LOSS MUTATED                                          0
  12Q LOSS WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  12Q LOSS MUTATED                                      4
  12Q LOSS WILD-TYPE                                   81
D65V8, multiclass
                                          clus
vv                                         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    4                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  12Q LOSS MUTATED    1  1  1  1
  12Q LOSS WILD-TYPE 62  6 11  4
D65V9, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0                1                 62
  R1                1                  6
  R2                1                 11
  RX                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"
D65V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0     3
  12Q LOSS WILD-TYPE     2                         1    73
D65V11, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    0  2
  12Q LOSS WILD-TYPE  8 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    2
  12Q LOSS WILD-TYPE    8   36
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 36
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   21 18
  13Q LOSS WILD-TYPE 36 15
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                39                 51 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                18                 15 
$`13Q LOSS MUTATED`
TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA 
       91.30        12.59        42.51        13.91        16.11        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH 
       18.12        57.53        99.88        69.21        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU 
       76.64        49.22        15.25        36.26        12.59         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB 
       66.51        72.39        32.68        16.37        11.31        24.36 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L6 
       83.80       153.63         4.11        58.55        60.89        28.31 
TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS 
       39.35        14.33        90.08        53.03        77.00        36.03 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5HA 
       38.50         0.00        39.48 

$`13Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       33.83        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JF TCGA-OR-A5JJ 
       12.00        88.87        19.04        44.45        66.25        16.11 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JX 
       67.59        18.48        39.25       121.25        29.82        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 
       18.15        27.02       108.13       113.92        35.57        49.08 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       24.62        46.49        88.01        95.18       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 
       44.84        12.85       152.15        31.79        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       23.64         5.23        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       36.33        61.08        79.07        61.05        28.04        18.05 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       24.85        20.25        22.32 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.00               5.23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            153.63             152.15 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             38.50              39.25 
[1] "0.0 - 153.6 (38.5)" "5.2 - 152.2 (39.2)"
[1] "hr=" "1.7"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         3       20         5        9
  13Q LOSS WILD-TYPE       6       23        13        9
D66V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  3                  6
  STAGE II                20                 23
  STAGE III                5                 13
  STAGE IV                 9                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS MUTATED    3 21  4  9
  13Q LOSS WILD-TYPE  6 27  7 11
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                3                  6
  T2               21                 27
  T3                4                  7
  T4                9                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   34  3
  13Q LOSS WILD-TYPE 44  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     34    3
  13Q LOSS WILD-TYPE   44    7
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               34                 44
  1                3                  7
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   24 15
  13Q LOSS WILD-TYPE 35 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     24   15
  13Q LOSS WILD-TYPE   35   16
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               24                 35
  MALE                 15                 16
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   29  7
  13Q LOSS WILD-TYPE 40 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     29    7
  13Q LOSS WILD-TYPE   40   11
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                29                 40
  YES                7                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  13Q LOSS MUTATED                                       1
  13Q LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  13Q LOSS MUTATED                                          3
  13Q LOSS WILD-TYPE                                        1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  13Q LOSS MUTATED                                     35
  13Q LOSS WILD-TYPE                                   50
D66V8, multiclass
                                          clus
vv                                         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                3                  1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   35                 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"
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED   25  4  5  2
  13Q LOSS WILD-TYPE 38  3  7  3
D66V9, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               25                 38
  R1                4                  3
  R2                5                  7
  RX                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"
D66V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         0    33
  13Q LOSS WILD-TYPE     2                         1    43
D66V11, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   33                 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"
D66V12, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2 13
  13Q LOSS WILD-TYPE  6 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   13
  13Q LOSS WILD-TYPE    6   25
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               13                 25
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   11  7
  14Q LOSS WILD-TYPE 46 26
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 72 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 26 
$`14Q LOSS MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JD TCGA-OR-A5JH 
       12.59        88.87        16.11        19.04        99.88        69.37 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5KQ 
       49.22        18.48        36.26        66.51        18.15        88.01 
TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LN TCGA-OR-A5LT TCGA-PK-A5HA 
        4.11        28.31         5.23        77.00        18.05        39.48 

$`14Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA 
       55.13        68.75        13.91        12.00        44.45        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI 
       18.12        57.53        69.21        66.25        17.79        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS 
       16.11        67.59        39.25        15.25       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       29.82         9.50        72.39        31.23        27.02       108.13 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       113.92        35.57        16.37        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        46.49        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        44.84        12.85        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD 
      152.15        31.79        29.10        28.64        23.64        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       21.76        14.63        52.24        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        53.03        61.08        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       36.03        38.50         0.00        24.85        20.25        22.32 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              4.11               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             99.88             153.63 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            32.285             39.300 
[1] "4.1 - 99.9 (32.3)"  "0.0 - 153.6 (39.3)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         1        9         3        5
  14Q LOSS WILD-TYPE       8       34        15       13
D67V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 9                 34
  STAGE III                3                 15
  STAGE IV                 5                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    1  9  3  5
  14Q LOSS WILD-TYPE  8 39  8 15
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                1                  8
  T2                9                 39
  T3                3                  8
  T4                5                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   17  1
  14Q LOSS WILD-TYPE 61  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     17    1
  14Q LOSS WILD-TYPE   61    9
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               17                 61
  1                1                  9
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   11  7
  14Q LOSS WILD-TYPE 48 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11    7
  14Q LOSS WILD-TYPE   48   24
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               11                 48
  MALE                  7                 24
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   14  4
  14Q LOSS WILD-TYPE 55 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     14    4
  14Q LOSS WILD-TYPE   55   14
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                14                 55
  YES                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  14Q LOSS MUTATED                                       1
  14Q LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  14Q LOSS MUTATED                                          2
  14Q LOSS WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  14Q LOSS MUTATED                                     15
  14Q LOSS WILD-TYPE                                   70
D67V8, multiclass
                                          clus
vv                                         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   15                 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"
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED   11  2  4  1
  14Q LOSS WILD-TYPE 52  5  8  4
D67V9, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               11                 52
  R1                2                  5
  R2                4                  8
  RX                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"
D67V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       0                         1    14
  14Q LOSS WILD-TYPE     2                         0    62
D67V11, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   14                 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"
D67V12, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    3  5
  14Q LOSS WILD-TYPE  5 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3    5
  14Q LOSS WILD-TYPE    5   33
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO                5                 33
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   13  8
  15Q LOSS WILD-TYPE 44 25
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                 69 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                 25 
$`15Q LOSS MUTATED`
TCGA-OR-A5KP TCGA-P6-A5OG TCGA-OR-A5J7 TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI 
       91.30        12.59        16.11        99.88        69.37        76.64 
TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KT 
       18.48        36.26        66.51        32.68        11.31        95.18 
TCGA-OR-A5KX TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LS TCGA-OR-A5LT 
       44.84        28.31         5.23        39.35        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5HA 
       38.50         0.00        39.48 

$`15Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       68.75        13.91        12.00        88.87        19.04        44.45 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        18.12        57.53        69.21        66.25        17.79 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       16.11        49.22        67.59        39.25        15.25       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       12.59        29.82         9.50        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       27.02       108.13       113.92        35.57        16.37        49.08 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU 
       24.62        24.36        46.49        88.01        83.80       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE 
      152.15        31.79        29.10        28.64        23.64        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        77.00        79.07        61.05        28.04 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       24.85        20.25        22.32 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.00               4.11 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             99.88             153.63 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             36.26              39.58 
[1] "0.0 - 99.9 (36.3)"  "4.1 - 153.6 (39.6)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         3        8         5        5
  15Q LOSS WILD-TYPE       6       35        13       13
D68V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  3                  6
  STAGE II                 8                 35
  STAGE III                5                 13
  STAGE IV                 5                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    3 10  2  6
  15Q LOSS WILD-TYPE  6 38  9 14
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                3                  6
  T2               10                 38
  T3                2                  9
  T4                6                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   19  2
  15Q LOSS WILD-TYPE 59  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19    2
  15Q LOSS WILD-TYPE   59    8
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               19                 59
  1                2                  8
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   15  6
  15Q LOSS WILD-TYPE 44 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     15    6
  15Q LOSS WILD-TYPE   44   25
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               15                 44
  MALE                  6                 25
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   19  2
  15Q LOSS WILD-TYPE 50 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19    2
  15Q LOSS WILD-TYPE   50   16
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                19                 50
  YES                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  15Q LOSS MUTATED                                       1
  15Q LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  15Q LOSS MUTATED                                          2
  15Q LOSS WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  15Q LOSS MUTATED                                     18
  15Q LOSS WILD-TYPE                                   67
D68V8, multiclass
                                          clus
vv                                         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   18                 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"
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   14  2  3  1
  15Q LOSS WILD-TYPE 49  5  9  4
D68V9, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               14                 49
  R1                2                  5
  R2                3                  9
  RX                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"
D68V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         0    18
  15Q LOSS WILD-TYPE     2                         1    58
D68V11, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   18                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  9
  15Q LOSS WILD-TYPE  7 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    9
  15Q LOSS WILD-TYPE    7   29
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                9                 29
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    0  4
  16P LOSS WILD-TYPE 57 29
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 86 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 29 
$`16P LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JY TCGA-OR-A5LD 
       16.11        18.12        18.15        39.35 

$`16P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        30.31        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       66.25        17.79        69.37        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       67.59        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.08        24.62        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LE 
       28.31        29.10        28.64        23.64         5.23        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        38.50         0.00        24.85        20.25 
TCGA-PK-A5HA TCGA-PK-A5HC 
       39.48        22.32 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             16.11               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             39.35             153.63 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            18.135             39.365 
[1] "16.1 - 39.4 (18.1)" "0.0 - 153.6 (39.4)"
[1] "hr=" "5.3"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         0        0         2        2
  16P LOSS WILD-TYPE       9       43        16       16
D69V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 0                 43
  STAGE III                2                 16
  STAGE IV                 2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16P LOSS MUTATED    0  0  1  3
  16P LOSS WILD-TYPE  9 48 10 17
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                  9
  T2                0                 48
  T3                1                 10
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3  1
  16P LOSS WILD-TYPE 75  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    1
  16P LOSS WILD-TYPE   75    9
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                3                 75
  1                1                  9
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  2
  16P LOSS WILD-TYPE 57 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    2
  16P LOSS WILD-TYPE   57   29
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  2                 29
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  1
  16P LOSS WILD-TYPE 67 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    1
  16P LOSS WILD-TYPE   67   17
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 2                 67
  YES                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  16P LOSS MUTATED                                       0
  16P LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  16P LOSS MUTATED                                          0
  16P LOSS WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  16P LOSS MUTATED                                      4
  16P LOSS WILD-TYPE                                   81
D69V8, multiclass
                                          clus
vv                                         16P LOSS MUTATED 16P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    4                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED    0  2  1  1
  16P LOSS WILD-TYPE 63  5 11  4
D69V9, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                0                 63
  R1                2                  5
  R2                1                 11
  RX                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"
D69V10, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 29 
        TCGA-OR-A5KP         TCGA-P6-A5OG         TCGA-OR-A5J2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-OR-A5J3         TCGA-OR-A5J4         TCGA-OR-A5J8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-OR-A5JG         TCGA-OR-A5JJ         TCGA-OR-A5JT 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JX         TCGA-OR-A5K2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-OR-A5K5         TCGA-OR-A5KB         TCGA-OR-A5KU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-OR-A5KV         TCGA-OR-A5KW         TCGA-OR-A5KY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LG         TCGA-OR-A5LL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-OR-A5LM         TCGA-OR-A5LN         TCGA-OR-A5LO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-OR-A5LP         TCGA-OR-A5LT         TCGA-OU-A5PI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-PK-A5HA         TCGA-PK-A5HC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         0     4
  16P LOSS WILD-TYPE     2                         1    72
D69V11, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  1
  16P LOSS WILD-TYPE  7 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    1
  16P LOSS WILD-TYPE    7   37
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                1                 37
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    1  4
  16Q LOSS WILD-TYPE 56 29
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 85 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 29 
$`16Q LOSS MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5LB TCGA-OR-A5J7 TCGA-OR-A5JY TCGA-OR-A5LD 
       33.83        39.58        16.11        18.15        39.35 

$`16Q LOSS WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        12.59        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       68.75        13.91        12.00        88.87        19.04        44.45 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       30.31        18.12        57.53        99.88        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        69.37        76.64        16.11        49.22        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       18.48        39.25        15.25        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
       29.82         9.50        66.51        72.39        31.23        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
      108.13        32.68       113.92        35.57        16.37        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        68.25        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF 
       29.10        28.64        23.64         5.23        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        36.33        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             16.11               0.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             39.58             153.63 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             33.83              39.25 
[1] "16.1 - 39.6 (33.8)" "0.0 - 153.6 (39.2)"
[1] "hr=" "3.3"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         0        1         2        2
  16Q LOSS WILD-TYPE       9       42        16       16
D70V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                2                 16
  STAGE IV                 2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED    0  1  1  3
  16Q LOSS WILD-TYPE  9 47 10 17
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                1                 10
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  1
  16Q LOSS WILD-TYPE 74  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    1
  16Q LOSS WILD-TYPE   74    9
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                4                 74
  1                1                  9
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  2
  16Q LOSS WILD-TYPE 56 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    2
  16Q LOSS WILD-TYPE   56   29
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 56
  MALE                  2                 29
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  2
  16Q LOSS WILD-TYPE 66 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    2
  16Q LOSS WILD-TYPE   66   16
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 3                 66
  YES                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  16Q LOSS MUTATED                                       0
  16Q LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  16Q LOSS MUTATED                                          0
  16Q LOSS WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  16Q LOSS MUTATED                                      5
  16Q LOSS WILD-TYPE                                   80
D70V8, multiclass
                                          clus
vv                                         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    5                 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"
                    vv
clus                 R0 R1 R2 RX
  16Q LOSS MUTATED    2  1  1  1
  16Q LOSS WILD-TYPE 61  6 11  4
D70V9, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0                2                 61
  R1                1                  6
  R2                1                 11
  RX                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"
D70V10, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 29 
        TCGA-OR-A5KP         TCGA-P6-A5OG         TCGA-OR-A5J2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-OR-A5J3         TCGA-OR-A5J4         TCGA-OR-A5J8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-OR-A5JG         TCGA-OR-A5JJ         TCGA-OR-A5JT 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JX         TCGA-OR-A5K2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-OR-A5K5         TCGA-OR-A5KB         TCGA-OR-A5KU 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-OR-A5KV         TCGA-OR-A5KW         TCGA-OR-A5KY 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LG         TCGA-OR-A5LL 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-OR-A5LM         TCGA-OR-A5LN         TCGA-OR-A5LO 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-OR-A5LP         TCGA-OR-A5LT         TCGA-OU-A5PI 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-PK-A5HA         TCGA-PK-A5HC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         0     5
  16Q LOSS WILD-TYPE     2                         1    71
D70V11, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    1  2
  16Q LOSS WILD-TYPE  7 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    2
  16Q LOSS WILD-TYPE    7   36
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 36
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   15 18
  17P LOSS WILD-TYPE 42 15
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                33                 57 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                18                 15 
$`17P LOSS MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5JA 
       91.30        39.58        12.59        42.51        16.11        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JK 
       18.12        57.53        69.21        17.79        69.37        49.22 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 
       18.48        15.25        12.59        66.51        72.39        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       16.37        11.31        95.18        44.84        12.85         4.11 
TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LM 
       60.89        28.31         5.23        21.76        14.33        61.08 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       36.03        38.50        39.48 

$`17P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       33.83        43.30        44.55        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JD TCGA-OR-A5JF 
       12.00        88.87        19.04        44.45        99.88        66.25 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       76.64        16.11        67.59        39.25        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
       29.82         9.50        31.23        18.15        27.02       108.13 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
      113.92        35.57        49.08        24.62        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L1 
       88.01        83.80       153.63       127.50        68.25        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD 
      152.15        31.79        29.10        28.64        23.64        39.35 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        90.08        53.03 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH 
       77.00        79.07        61.05        28.04        18.05         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       24.85        20.25        22.32 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              4.11               0.00 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             95.18             153.63 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             32.68              43.30 
[1] "4.1 - 95.2 (32.7)"  "0.0 - 153.6 (43.3)"
[1] "hr=" "2.7"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         3       13         4       11
  17P LOSS WILD-TYPE       6       30        14        7
D71V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  3                  6
  STAGE II                13                 30
  STAGE III                4                 14
  STAGE IV                11                  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"
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    3 15  2 11
  17P LOSS WILD-TYPE  6 33  9  9
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                3                  6
  T2               15                 33
  T3                2                  9
  T4               11                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   27  4
  17P LOSS WILD-TYPE 51  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     27    4
  17P LOSS WILD-TYPE   51    6
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               27                 51
  1                4                  6
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   19 14
  17P LOSS WILD-TYPE 40 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     19   14
  17P LOSS WILD-TYPE   40   17
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               19                 40
  MALE                 14                 17
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   22  8
  17P LOSS WILD-TYPE 47 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     22    8
  17P LOSS WILD-TYPE   47   10
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                22                 47
  YES                8                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  17P LOSS MUTATED                                       0
  17P LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  17P LOSS MUTATED                                          1
  17P LOSS WILD-TYPE                                        3
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  17P LOSS MUTATED                                     32
  17P LOSS WILD-TYPE                                   53
D71V8, multiclass
                                          clus
vv                                         17P LOSS MUTATED 17P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                1                  3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   32                 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"
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   19  5  5  1
  17P LOSS WILD-TYPE 44  2  7  4
D71V9, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               19                 44
  R1                5                  2
  R2                5                  7
  RX                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"
D71V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         0    29
  17P LOSS WILD-TYPE     2                         1    47
D71V11, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   29                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1 13
  17P LOSS WILD-TYPE  7 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   13
  17P LOSS WILD-TYPE    7   25
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               13                 25
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   13 12
  17Q LOSS WILD-TYPE 44 21
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                 65 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 21 
$`17Q LOSS MUTATED`
TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC 
       39.58        12.59        42.51        16.11        30.31        57.53 
TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW 
       17.79        49.22        15.25        12.59        66.51        72.39 
TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L6 
       32.68        11.31        95.18        12.85         4.11        28.31 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LM TCGA-OR-A5LS TCGA-OU-A5PI 
        5.23        21.76        52.24        61.08        36.03        38.50 
TCGA-PK-A5HA 
       39.48 

$`17Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       33.83        91.30        43.30        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB 
       13.91        12.00        88.87        19.04        44.45        18.12 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       99.88        69.21        66.25        69.37        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       67.59        18.48        39.25        36.26       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
        9.50        31.23        18.15        27.02       108.13       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
       35.57        16.37        49.08        24.62        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       88.01        83.80       153.63       127.50        68.25        44.84 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55        60.89       152.15        31.79        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       23.64        39.35        14.63        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        53.03        77.00        79.07        61.05        28.04 
TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       18.05         0.00        24.85        20.25        22.32 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              4.11               0.00 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             95.18             153.63 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             32.68              43.30 
[1] "4.1 - 95.2 (32.7)"  "0.0 - 153.6 (43.3)"
[1] "hr=" "2.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         2       10         3        8
  17Q LOSS WILD-TYPE       7       33        15       10
D72V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  2                  7
  STAGE II                10                 33
  STAGE III                3                 15
  STAGE IV                 8                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    2 11  2  8
  17Q LOSS WILD-TYPE  7 37  9 12
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                2                  7
  T2               11                 37
  T3                2                  9
  T4                8                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   20  3
  17Q LOSS WILD-TYPE 58  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     20    3
  17Q LOSS WILD-TYPE   58    7
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               20                 58
  1                3                  7
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   11 14
  17Q LOSS WILD-TYPE 48 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     11   14
  17Q LOSS WILD-TYPE   48   17
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               11                 48
  MALE                 14                 17
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   17  6
  17Q LOSS WILD-TYPE 52 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     17    6
  17Q LOSS WILD-TYPE   52   12
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                17                 52
  YES                6                 12
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  17Q LOSS MUTATED                                       0
  17Q LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  17Q LOSS MUTATED                                          0
  17Q LOSS WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  17Q LOSS MUTATED                                     25
  17Q LOSS WILD-TYPE                                   60
D72V8, multiclass
                                          clus
vv                                         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   25                 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"
                    vv
clus                 R0 R1 R2 RX
  17Q LOSS MUTATED   13  3  4  2
  17Q LOSS WILD-TYPE 50  4  8  3
D72V9, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               13                 50
  R1                3                  4
  R2                4                  8
  RX                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"
D72V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0    21
  17Q LOSS WILD-TYPE     2                         1    55
D72V11, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   21                 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"
D72V12, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1 10
  17Q LOSS WILD-TYPE  7 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   10
  17Q LOSS WILD-TYPE    7   28
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               10                 28
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   23 14
  18P LOSS WILD-TYPE 34 19
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 53 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                14                 19 
$`18P LOSS MUTATED`
TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA 
       91.30        12.59        42.51        88.87        16.11        30.31 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        99.88        17.79        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        15.25        36.26        12.59        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KO 
       72.39        31.23        18.15        32.68        16.37        46.49 
TCGA-OR-A5KT TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LL 
       95.18        12.85        28.31         5.23        21.76        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.08        77.00        36.03        18.05        38.50         0.00 
TCGA-PK-A5HA 
       39.48 

$`18P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       33.83        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JE TCGA-OR-A5JF 
       13.91        12.00        19.04        44.45        69.21        66.25 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JU 
       16.11        67.59        18.48        39.25       121.25         9.50 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 
       27.02       108.13       113.92        35.57        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV 
       11.31        24.36        88.01        83.80       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       68.25        44.84         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF 
       31.79        29.10        28.64        23.64        39.35        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO 
       52.24        78.41        14.33        36.33        90.08        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       61.05        28.04        24.85        20.25        22.32 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.00               4.11 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             99.88             153.63 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             36.03              39.58 
[1] "0.0 - 99.9 (36.0)"  "4.1 - 153.6 (39.6)"
[1] "hr=" "1.2"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         3       16         5       11
  18P LOSS WILD-TYPE       6       27        13        7
D73V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  3                  6
  STAGE II                16                 27
  STAGE III                5                 13
  STAGE IV                11                  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"
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    3 17  4 11
  18P LOSS WILD-TYPE  6 31  7  9
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                3                  6
  T2               17                 31
  T3                4                  7
  T4               11                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   31  4
  18P LOSS WILD-TYPE 47  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     31    4
  18P LOSS WILD-TYPE   47    6
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               31                 47
  1                4                  6
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   22 15
  18P LOSS WILD-TYPE 37 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     22   15
  18P LOSS WILD-TYPE   37   16
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               22                 37
  MALE                 15                 16
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   25  9
  18P LOSS WILD-TYPE 44  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     25    9
  18P LOSS WILD-TYPE   44    9
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                25                 44
  YES                9                  9
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  18P LOSS MUTATED                                       1
  18P LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  18P LOSS MUTATED                                          2
  18P LOSS WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  18P LOSS MUTATED                                     34
  18P LOSS WILD-TYPE                                   51
D73V8, multiclass
                                          clus
vv                                         18P LOSS MUTATED 18P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   34                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   24  4  6  0
  18P LOSS WILD-TYPE 39  3  6  5
D73V9, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               24                 39
  R1                4                  3
  R2                6                  6
  RX                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"
D73V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         1    29
  18P LOSS WILD-TYPE     2                         0    47
D73V11, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   29                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2 10
  18P LOSS WILD-TYPE  6 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   10
  18P LOSS WILD-TYPE    6   28
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               10                 28
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   23 12
  18Q LOSS WILD-TYPE 34 21
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                35                 55 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                12                 21 
$`18Q LOSS MUTATED`
TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB 
       91.30        12.59        42.51        88.87        16.11        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        99.88        17.79        69.37        76.64        49.22 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        36.26        12.59        29.82        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5KY TCGA-OR-A5L6 
       31.23        18.15        32.68        46.49        12.85        28.31 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
        5.23        21.76        52.24        53.03        61.08        77.00 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5HA 
       36.03        18.05        38.50         0.00        39.48 

$`18Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       33.83        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JE 
       13.91        12.00        19.04        44.45        30.31        69.21 
TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR 
       66.25        16.11        67.59        18.48        39.25       121.25 
TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        9.50        27.02       108.13       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KS 
       49.08        24.62        11.31        24.36        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        68.25        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55        60.89       152.15        31.79        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       23.64        39.35        14.63        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5H9 
       90.08        79.07        61.05        28.04        24.85        20.25 
TCGA-PK-A5HC 
       22.32 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.00               4.11 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             99.88             153.63 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             36.26              39.35 
[1] "0.0 - 99.9 (36.3)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "1"  
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         2       16         5       10
  18Q LOSS WILD-TYPE       7       27        13        8
D74V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  2                  7
  STAGE II                16                 27
  STAGE III                5                 13
  STAGE IV                10                  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"
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    2 17  4 10
  18Q LOSS WILD-TYPE  7 31  7 10
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                2                  7
  T2               17                 31
  T3                4                  7
  T4               10                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   29  4
  18Q LOSS WILD-TYPE 49  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     29    4
  18Q LOSS WILD-TYPE   49    6
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               29                 49
  1                4                  6
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   19 16
  18Q LOSS WILD-TYPE 40 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     19   16
  18Q LOSS WILD-TYPE   40   15
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               19                 40
  MALE                 16                 15
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   24  8
  18Q LOSS WILD-TYPE 45 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     24    8
  18Q LOSS WILD-TYPE   45   10
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                24                 45
  YES                8                 10
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  18Q LOSS MUTATED                                       1
  18Q LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  18Q LOSS MUTATED                                          2
  18Q LOSS WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  18Q LOSS MUTATED                                     32
  18Q LOSS WILD-TYPE                                   53
D74V8, multiclass
                                          clus
vv                                         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   32                 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"
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED   22  3  6  1
  18Q LOSS WILD-TYPE 41  4  6  4
D74V9, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               22                 41
  R1                3                  4
  R2                6                  6
  RX                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"
D74V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         1    27
  18Q LOSS WILD-TYPE     2                         0    49
D74V11, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   27                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2 10
  18Q LOSS WILD-TYPE  6 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   10
  18Q LOSS WILD-TYPE    6   28
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               10                 28
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    1  4
  19P LOSS WILD-TYPE 56 29
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 85 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 29 
$`19P LOSS MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5KB TCGA-OR-A5LI 
       12.59        44.55        18.12        24.36        14.33 

$`19P LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J2 
       33.83        91.30        43.30        39.58        42.51        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       44.45        30.31        57.53        99.88        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        69.37        76.64        16.11        49.22        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       18.48        39.25        15.25        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       49.08        24.62        11.31        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        68.25        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             12.59               0.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             44.55             153.63 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             18.12              39.35 
[1] "12.6 - 44.5 (18.1)" "0.0 - 153.6 (39.4)"
[1] "hr=" "4.4"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         0        2         0        3
  19P LOSS WILD-TYPE       9       41        18       15
D75V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 2                 41
  STAGE III                0                 18
  STAGE IV                 3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    0  2  0  3
  19P LOSS WILD-TYPE  9 46 11 17
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                0                  9
  T2                2                 46
  T3                0                 11
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    5  0
  19P LOSS WILD-TYPE 73 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      5    0
  19P LOSS WILD-TYPE   73   10
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                5                 73
  1                0                 10
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    3  2
  19P LOSS WILD-TYPE 56 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    2
  19P LOSS WILD-TYPE   56   29
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                3                 56
  MALE                  2                 29
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    4  0
  19P LOSS WILD-TYPE 65 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4    0
  19P LOSS WILD-TYPE   65   18
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 4                 65
  YES                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  19P LOSS MUTATED                                       0
  19P LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  19P LOSS MUTATED                                          0
  19P LOSS WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  19P LOSS MUTATED                                      5
  19P LOSS WILD-TYPE                                   80
D75V8, multiclass
                                          clus
vv                                         19P LOSS MUTATED 19P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    5                 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"
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED    2  1  2  0
  19P LOSS WILD-TYPE 61  6 10  5
D75V9, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                2                 61
  R1                1                  6
  R2                2                 10
  RX                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"
D75V10, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 29 
        TCGA-OR-A5KP         TCGA-OR-A5J2         TCGA-OR-A5J3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J7         TCGA-OR-A5J8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-OR-A5JG         TCGA-OR-A5JJ         TCGA-OR-A5JT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-OR-A5JV         TCGA-OR-A5JX         TCGA-OR-A5JY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-OR-A5K2         TCGA-OR-A5K5         TCGA-OR-A5KU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-OR-A5KV         TCGA-OR-A5KW         TCGA-OR-A5KY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LG         TCGA-OR-A5LL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-OR-A5LM         TCGA-OR-A5LN         TCGA-OR-A5LO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-OR-A5LP         TCGA-OR-A5LT         TCGA-OU-A5PI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-PK-A5HA         TCGA-PK-A5HC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         0     5
  19P LOSS WILD-TYPE     2                         1    71
D75V11, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    0  3
  19P LOSS WILD-TYPE  8 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    3
  19P LOSS WILD-TYPE    8   35
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                3                 35
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    1  3
  19Q LOSS WILD-TYPE 56 30
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 86 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 30 
$`19Q LOSS MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5KB TCGA-OR-A5LL 
       12.59        44.55        24.36        53.03 

$`19Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J2 
       33.83        91.30        43.30        39.58        42.51        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       44.45        30.31        18.12        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       66.25        17.79        69.37        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       67.59        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KQ 
       16.37        49.08        24.62        11.31        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        29.10        28.64        23.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       21.76        14.63        52.24        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        38.50         0.00        24.85        20.25 
TCGA-PK-A5HA TCGA-PK-A5HC 
       39.48        22.32 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             12.59               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             53.03             153.63 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            34.455             38.875 
[1] "12.6 - 53.0 (34.5)" "0.0 - 153.6 (38.9)"
[1] "hr=" "2.8"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0        3         0        1
  19Q LOSS WILD-TYPE       9       40        18       17
D76V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 3                 40
  STAGE III                0                 18
  STAGE IV                 1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    0  3  0  1
  19Q LOSS WILD-TYPE  9 45 11 19
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                0                  9
  T2                3                 45
  T3                0                 11
  T4                1                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    4  0
  19Q LOSS WILD-TYPE 74 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    0
  19Q LOSS WILD-TYPE   74   10
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                4                 74
  1                0                 10
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  1
  19Q LOSS WILD-TYPE 56 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    1
  19Q LOSS WILD-TYPE   56   30
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 56
  MALE                  1                 30
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    4  0
  19Q LOSS WILD-TYPE 65 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    0
  19Q LOSS WILD-TYPE   65   18
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 4                 65
  YES                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  19Q LOSS MUTATED                                       0
  19Q LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  19Q LOSS MUTATED                                          0
  19Q LOSS WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  19Q LOSS MUTATED                                      4
  19Q LOSS WILD-TYPE                                   81
D76V8, multiclass
                                          clus
vv                                         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    4                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  19Q LOSS MUTATED    3  0  1  0
  19Q LOSS WILD-TYPE 60  7 11  5
D76V9, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                3                 60
  R1                0                  7
  R2                1                 11
  RX                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"
D76V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     3
  19Q LOSS WILD-TYPE     2                         1    73
D76V11, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    0  2
  19Q LOSS WILD-TYPE  8 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    2
  19Q LOSS WILD-TYPE    8   36
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 36
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    6  3
  20P LOSS WILD-TYPE 51 30
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 81 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 30 
$`20P LOSS MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JM 
       33.83        91.30        42.51        16.11        30.31        18.48 
TCGA-OR-A5JS TCGA-OU-A5PI TCGA-PK-A5HC 
       12.59        38.50        22.32 

$`20P LOSS WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        12.59        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB 
       13.91        12.00        88.87        19.04        44.45        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       57.53        99.88        69.21        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP 
       76.64        16.11        49.22        67.59        39.25        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
       36.26       121.25        29.82         9.50        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       35.57        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       68.25        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        28.31        29.10        28.64        23.64 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
        5.23        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       14.33        36.33        90.08        53.03        61.08        77.00 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OH 
       79.07        61.05        28.04        36.03        18.05         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       24.85        20.25        39.48 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             12.59               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             91.30             153.63 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             30.31              39.48 
[1] "12.6 - 91.3 (30.3)" "0.0 - 153.6 (39.5)"
[1] "hr=" "1.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         0        3         2        3
  20P LOSS WILD-TYPE       9       40        16       15
D77V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 3                 40
  STAGE III                2                 16
  STAGE IV                 3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    0  4  1  3
  20P LOSS WILD-TYPE  9 44 10 17
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                0                  9
  T2                4                 44
  T3                1                 10
  T4                3                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    7  1
  20P LOSS WILD-TYPE 71  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      7    1
  20P LOSS WILD-TYPE   71    9
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                7                 71
  1                1                  9
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    8  1
  20P LOSS WILD-TYPE 51 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8    1
  20P LOSS WILD-TYPE   51   30
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                 51
  MALE                  1                 30
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    6  3
  20P LOSS WILD-TYPE 63 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    3
  20P LOSS WILD-TYPE   63   15
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 6                 63
  YES                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  20P LOSS MUTATED                                       0
  20P LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  20P LOSS MUTATED                                          0
  20P LOSS WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  20P LOSS MUTATED                                      9
  20P LOSS WILD-TYPE                                   76
D77V8, multiclass
                                          clus
vv                                         20P LOSS MUTATED 20P LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    9                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  20P LOSS MUTATED    3  4  0  0
  20P LOSS WILD-TYPE 60  3 12  5
D77V9, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                3                 60
  R1                4                  3
  R2                0                 12
  RX                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"
D77V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       1                         0     7
  20P LOSS WILD-TYPE     1                         1    69
D77V11, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    7                 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"
D77V12, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  3
  20P LOSS WILD-TYPE  7 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    3
  20P LOSS WILD-TYPE    7   35
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                3                 35
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE 56 31
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 87 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 31 
$`20Q LOSS MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J7 TCGA-OR-A5JA 
       91.30        16.11        30.31 

$`20Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        43.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       55.13        68.75        13.91        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       44.45        18.12        57.53        99.88        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        69.37        76.64        16.11        49.22        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       18.48        39.25        15.25        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.08        24.62        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        29.10        28.64        23.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       21.76        14.63        52.24        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       90.08        53.03        61.08        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG 
       28.04        36.03        18.05        38.50         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       20.25        39.48        22.32 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             16.11               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             91.30             153.63 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             30.31              39.25 
[1] "16.1 - 91.3 (30.3)" "0.0 - 153.6 (39.2)"
[1] "hr=" "1.8"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         0        1         1        1
  20Q LOSS WILD-TYPE       9       42        17       17
D78V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                1                 17
  STAGE IV                 1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20Q LOSS MUTATED    0  1  1  1
  20Q LOSS WILD-TYPE  9 47 10 19
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                1                 10
  T4                1                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V5, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  0
  20Q LOSS WILD-TYPE 75 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE   75   10
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                3                 75
  1                0                 10
[1] 2 2
[1] FALSE
D78V6, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  0
  20Q LOSS WILD-TYPE 56 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE   56   31
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                 56
  MALE                  0                 31
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  0
  20Q LOSS WILD-TYPE 66 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE   66   18
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 3                 66
  YES                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                     1
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  20Q LOSS MUTATED                                          0
  20Q LOSS WILD-TYPE                                        4
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  20Q LOSS MUTATED                                      3
  20Q LOSS WILD-TYPE                                   82
D78V8, multiclass
                                          clus
vv                                         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   0                  1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                0                  4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                    3                 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"
                    vv
clus                 R0 R1 R2 RX
  20Q LOSS MUTATED    1  2  0  0
  20Q LOSS WILD-TYPE 62  5 12  5
D78V9, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                1                 62
  R1                2                  5
  R2                0                 12
  RX                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"
D78V10, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 29 
        TCGA-P6-A5OG         TCGA-OR-A5J2         TCGA-OR-A5J3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-OR-A5J4         TCGA-OR-A5J8         TCGA-OR-A5JG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JT         TCGA-OR-A5JV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-OR-A5JX         TCGA-OR-A5JY         TCGA-OR-A5K2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-OR-A5K5         TCGA-OR-A5KB         TCGA-OR-A5KU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-OR-A5KV         TCGA-OR-A5KW         TCGA-OR-A5KY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-OR-A5L9         TCGA-OR-A5LG         TCGA-OR-A5LL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-OR-A5LM         TCGA-OR-A5LN         TCGA-OR-A5LO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-OR-A5LP         TCGA-OR-A5LT         TCGA-OU-A5PI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-PK-A5HA         TCGA-PK-A5HC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     3
  20Q LOSS WILD-TYPE     2                         1    73
D78V11, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  1
  20Q LOSS WILD-TYPE  7 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    1
  20Q LOSS WILD-TYPE    7   37
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                1                 37
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    6  9
  21Q LOSS WILD-TYPE 51 24
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 75 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                 24 
$`21Q LOSS MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JM 
       12.59        19.04        30.31        99.88        69.37        18.48 
TCGA-OR-A5JQ TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5LC TCGA-OR-A5LE 
       36.26         9.50        66.51        18.15         5.23        21.76 
TCGA-OR-A5LF TCGA-OR-A5LN TCGA-PK-A5HA 
       14.63        77.00        39.48 

$`21Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        18.12        57.53        69.21        66.25        17.79 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP 
       76.64        16.11        49.22        67.59        39.25        15.25 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
      121.25        12.59        29.82        72.39        31.23        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
      108.13        32.68       113.92        35.57        16.37        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        68.25        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LG TCGA-OR-A5LH 
       29.10        28.64        23.64        39.35        52.24        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       14.33        36.33        90.08        53.03        61.08        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       24.85        20.25        22.32 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              5.23               0.00 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             99.88             153.63 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             21.76              39.58 
[1] "5.2 - 99.9 (21.8)"  "0.0 - 153.6 (39.6)"
[1] "hr=" "2.4"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         1        6         3        5
  21Q LOSS WILD-TYPE       8       37        15       13
D79V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 6                 37
  STAGE III                3                 15
  STAGE IV                 5                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    1  6  3  5
  21Q LOSS WILD-TYPE  8 42  8 15
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                1                  8
  T2                6                 42
  T3                3                  8
  T4                5                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   14  1
  21Q LOSS WILD-TYPE 64  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     14    1
  21Q LOSS WILD-TYPE   64    9
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               14                 64
  1                1                  9
[1] 2 2
[1] FALSE
D79V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   11  4
  21Q LOSS WILD-TYPE 48 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     11    4
  21Q LOSS WILD-TYPE   48   27
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               11                 48
  MALE                  4                 27
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   11  4
  21Q LOSS WILD-TYPE 58 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     11    4
  21Q LOSS WILD-TYPE   58   14
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                11                 58
  YES                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  21Q LOSS MUTATED                                       1
  21Q LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  21Q LOSS MUTATED                                          2
  21Q LOSS WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  21Q LOSS MUTATED                                     12
  21Q LOSS WILD-TYPE                                   73
D79V8, multiclass
                                          clus
vv                                         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   12                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   10  2  3  0
  21Q LOSS WILD-TYPE 53  5  9  5
D79V9, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               10                 53
  R1                2                  5
  R2                3                  9
  RX                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"
D79V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       0                         0    13
  21Q LOSS WILD-TYPE     2                         1    63
D79V11, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   13                 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"
D79V12, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    1  4
  21Q LOSS WILD-TYPE  7 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1    4
  21Q LOSS WILD-TYPE    7   34
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                4                 34
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   24 24
  22Q LOSS WILD-TYPE 33  9
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                48                 42 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                24                  9 
$`22Q LOSS MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        39.58        12.59        44.55        55.13        68.75 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB 
       88.87        16.11        19.04        44.45        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       57.53        99.88        69.21        17.79        69.37        76.64 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JU TCGA-OR-A5JV 
       49.22        15.25        36.26       121.25         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 
       72.39        31.23        18.15        32.68        16.37        11.31 
TCGA-OR-A5KQ TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LC 
       88.01        44.84        12.85         4.11        28.31         5.23 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       39.35        14.63        14.33        53.03        61.08        77.00 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA 
       36.03        18.05        38.50         0.00        20.25        39.48 

$`22Q LOSS WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JF 
       33.83        43.30        42.51        13.91        12.00        66.25 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JT 
       16.11        67.59        18.48        39.25        12.59        29.82 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 
       27.02       108.13       113.92        35.57        49.08        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        46.49        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 
       68.25        58.55        60.89       152.15        31.79        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       28.64        23.64        21.76        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5HC 
       90.08        79.07        61.05        28.04        24.85        22.32 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 0                 12 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            121.25             153.63 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             37.38              40.88 
[1] "0.0 - 121.2 (37.4)"  "12.0 - 153.6 (40.9)"
[1] "hr=" "2.8"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         4       19        11       13
  22Q LOSS WILD-TYPE       5       24         7        5
D80V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  4                  5
  STAGE II                19                 24
  STAGE III               11                  7
  STAGE IV                13                  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                 T1 T2 T3 T4
  22Q LOSS MUTATED    4 21  9 13
  22Q LOSS WILD-TYPE  5 27  2  7
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                4                  5
  T2               21                 27
  T3                9                  2
  T4               13                  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"
D80V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   42  5
  22Q LOSS WILD-TYPE 36  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     42    5
  22Q LOSS WILD-TYPE   36    5
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               42                 36
  1                5                  5
[1] 2 2
[1] FALSE
D80V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   29 19
  22Q LOSS WILD-TYPE 30 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     29   19
  22Q LOSS WILD-TYPE   30   12
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               29                 30
  MALE                 19                 12
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   36  9
  22Q LOSS WILD-TYPE 33  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     36    9
  22Q LOSS WILD-TYPE   33    9
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                36                 33
  YES                9                  9
[1] 2 2
[1] FALSE
                    vv
clus                 ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  22Q LOSS MUTATED                                       1
  22Q LOSS WILD-TYPE                                     0
                    vv
clus                 ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  22Q LOSS MUTATED                                          2
  22Q LOSS WILD-TYPE                                        2
                    vv
clus                 ADRENOCORTICAL CARCINOMA- USUAL TYPE
  22Q LOSS MUTATED                                     45
  22Q LOSS WILD-TYPE                                   40
D80V8, multiclass
                                          clus
vv                                         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                   1                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                2                  2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                   45                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   32  4  8  2
  22Q LOSS WILD-TYPE 31  3  4  3
D80V9, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               32                 31
  R1                4                  3
  R2                8                  4
  RX                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"
D80V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    40
  22Q LOSS WILD-TYPE     1                         0    36
D80V11, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   40                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    6 15
  22Q LOSS WILD-TYPE  2 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   15
  22Q LOSS WILD-TYPE    2   23
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO               15                 23
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED   11  5
  XP LOSS WILD-TYPE 46 28
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               16                74 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5                28 
$`XP LOSS MUTATED`
TCGA-OR-A5K0 TCGA-PK-A5HB TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JS TCGA-OR-A5JW 
       33.83        42.51        18.12        99.88        12.59        72.39 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5LE TCGA-OR-A5LG 
       49.08        11.31        24.36       127.50        21.76        52.24 
TCGA-OR-A5LI TCGA-OR-A5LL TCGA-PK-A5HA TCGA-PK-A5HC 
       14.33        53.03        39.48        22.32 

$`XP LOSS WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        12.59        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        30.31        57.53        69.21        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM 
       69.37        76.64        16.11        49.22        67.59        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       39.25        15.25        36.26       121.25        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       66.51        31.23        18.15        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ 
      113.92        35.57        16.37        24.62        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       83.80        95.18       153.63        68.25        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF 
       29.10        28.64        23.64         5.23        39.35        14.63 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        36.33        90.08        61.08        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 
       24.85        20.25 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
            11.31              0.00 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           127.50            153.63 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           36.655            38.875 
[1] "11.3 - 127.5 (36.7)" "0.0 - 153.6 (38.9)" 
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED         1        9         3        2
  XP LOSS WILD-TYPE       8       34        15       16
D81V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                9                34
  STAGE III               3                15
  STAGE IV                2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XP LOSS MUTATED    1 10  1  3
  XP LOSS WILD-TYPE  8 38 10 17
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               1                 8
  T2              10                38
  T3               1                10
  T4               3                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V5, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   14  1
  XP LOSS WILD-TYPE 64  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     14    1
  XP LOSS WILD-TYPE   64    9
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              14                64
  1               1                 9
[1] 2 2
[1] FALSE
D81V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   10  6
  XP LOSS WILD-TYPE 49 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     10    6
  XP LOSS WILD-TYPE   49   25
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              10                49
  MALE                 6                25
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   11  4
  XP LOSS WILD-TYPE 58 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     11    4
  XP LOSS WILD-TYPE   58   14
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               11                58
  YES               4                14
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  XP LOSS MUTATED                                       0
  XP LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  XP LOSS MUTATED                                          1
  XP LOSS WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  XP LOSS MUTATED                                     15
  XP LOSS WILD-TYPE                                   70
D81V8, multiclass
                                          clus
vv                                         XP LOSS MUTATED XP LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  15                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"
                   vv
clus                R0 R1 R2 RX
  XP LOSS MUTATED   11  2  1  1
  XP LOSS WILD-TYPE 52  5 11  4
D81V9, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              11                52
  R1               2                 5
  R2               1                11
  RX               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"
D81V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       1                         0    12
  XP LOSS WILD-TYPE     1                         1    64
D81V11, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  12                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"
D81V12, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    0  7
  XP LOSS WILD-TYPE  8 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0    7
  XP LOSS WILD-TYPE    8   31
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               7                31
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   10  6
  XQ LOSS WILD-TYPE 47 27
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16                74 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6                27 
$`XQ LOSS MUTATED`
TCGA-OR-A5K0 TCGA-PK-A5HB TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JS TCGA-OR-A5JW 
       33.83        42.51        18.12        99.88        12.59        72.39 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L2 TCGA-OR-A5LE 
       49.08        11.31       127.50        68.25        60.89        21.76 
TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-PK-A5HC 
       52.24        14.33        53.03        22.32 

$`XQ LOSS WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        12.59        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        13.91        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        30.31        57.53        69.21        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM 
       69.37        76.64        16.11        49.22        67.59        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       39.25        15.25        36.26       121.25        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       66.51        31.23        18.15        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
      113.92        35.57        16.37        24.62        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY 
       88.01        83.80        95.18       153.63        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11        58.55       152.15        31.79        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH 
       28.64        23.64         5.23        39.35        14.63        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        90.08        61.08        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG 
       28.04        36.03        18.05        38.50         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            11.31              0.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           127.50            153.63 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           45.795            37.415 
[1] "11.3 - 127.5 (45.8)" "0.0 - 153.6 (37.4)" 
[1] "hr=" "1"  
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         0        9         4        2
  XQ LOSS WILD-TYPE       9       34        14       16
D82V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II                9                34
  STAGE III               4                14
  STAGE IV                2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    0 11  1  3
  XQ LOSS WILD-TYPE  9 37 10 17
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               0                 9
  T2              11                37
  T3               1                10
  T4               3                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   13  2
  XQ LOSS WILD-TYPE 65  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13    2
  XQ LOSS WILD-TYPE   65    8
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              13                65
  1               2                 8
[1] 2 2
[1] FALSE
D82V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   11  5
  XQ LOSS WILD-TYPE 48 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11    5
  XQ LOSS WILD-TYPE   48   26
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              11                48
  MALE                 5                26
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   10  5
  XQ LOSS WILD-TYPE 59 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     10    5
  XQ LOSS WILD-TYPE   59   13
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               10                59
  YES               5                13
[1] 2 2
[1] FALSE
                   vv
clus                ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  XQ LOSS MUTATED                                       0
  XQ LOSS WILD-TYPE                                     1
                   vv
clus                ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  XQ LOSS MUTATED                                          1
  XQ LOSS WILD-TYPE                                        3
                   vv
clus                ADRENOCORTICAL CARCINOMA- USUAL TYPE
  XQ LOSS MUTATED                                     15
  XQ LOSS WILD-TYPE                                   70
D82V8, multiclass
                                          clus
vv                                         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                  0                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE               1                 3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                  15                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"
                   vv
clus                R0 R1 R2 RX
  XQ LOSS MUTATED   11  2  1  1
  XQ LOSS WILD-TYPE 52  5 11  4
D82V9, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              11                52
  R1               2                 5
  R2               1                11
  RX               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"
D82V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         0    13
  XQ LOSS WILD-TYPE     1                         1    63
D82V11, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  13                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"
D82V12, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    0  8
  XQ LOSS WILD-TYPE  8 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    8
  XQ LOSS WILD-TYPE    8   30
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               8                30
[1] 2 2
[1] FALSE
