[1] "ofn"        "-oTKIRP-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/KIRP-TP/22507257/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/22533934/transformed.cor.cli.txt"

nPatients in clinical file=291, in cluster file=288, common to both=288
[1] "Reduce the number of clustering variables from 82 to 74."
[1]  74 288
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10               278 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10               278 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               17               271 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               17               271 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               42               246 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               42               246 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               47               241 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               47               241 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               75               213 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               75               213 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               95               193 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               95               193 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               278 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               278 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               279 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               279 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               34               254 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               34               254 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               31               257 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               31               257 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               278 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               278 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                7               281 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                7               281 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              171               117 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              171               117 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              172               116 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              172               116 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               20               268 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               20               268 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               25               263 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               25               263 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               285 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               285 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                280 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                280 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                280 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                280 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                276 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                276 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                278 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                278 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               112                176 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               112                176 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               112                176 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               112                176 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                28                260 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                28                260 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                285 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                285 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                283 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                283 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               153                135 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               153                135 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               148                140 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               148                140 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               172                116 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               172                116 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               191                 97 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               191                 97 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                276 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                276 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                279 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                279 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                283 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                283 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                283 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                283 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                99                189 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                99                189 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               101                187 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               101                187 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                269 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                269 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                283 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                283 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               88               200 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               88               200 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               92               196 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               92               196 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               30               258 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               30               258 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21               267 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21               267 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               283 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               283 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3               285 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3               285 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21               267 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21               267 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               282 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               282 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               25               263 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               25               263 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               26               262 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               26               262 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               281 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               281 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8               280 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8               280 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               21               267 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               21               267 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               27               261 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               27               261 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16               272 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16               272 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               279 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               279 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               33               255 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               33               255 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               34               254 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               34               254 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                271 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                271 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                18                270 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                18                270 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                17                271 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                17                271 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                267 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                267 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                24                264 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                24                264 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                47                241 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                47                241 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                31                257 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                31                257 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                284 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                284 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                281 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                281 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                275 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                275 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                42                246 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                42                246 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                44                244 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                44                244 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                272 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                272 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                273 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                273 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                43                245 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                43                245 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                60                228 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                60                228 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               33               255 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               33               255 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               29               259 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               29               259 
[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] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 288 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=44,	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=230,	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=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "206"   "1"    
freq.contrast "1"     "206"  
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 288 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"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=54, 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 
191  33  60   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  191    33    62 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
191  33  60   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  191    33    62 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
49 24  4 
[1] "table(vv)"
vv
N0 N1 N2 
49 24  4 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
49 24  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
49 24  4 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=36, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=34, binary=FALSE, numeric=TRUE
RACE, nv=4, 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     4   6
  1P GAIN WILD-TYPE 237  38
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10               275 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6                38 
$`1P GAIN MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-5P-A9K9 TCGA-BQ-5893 TCGA-G7-6789 TCGA-G7-A8LD 
       12.99        49.25        19.36         7.92         4.01        16.90 
TCGA-GL-7966 TCGA-HE-7130 TCGA-IA-A40Y TCGA-WN-A9G9 
        3.68        58.19         2.04        26.01 

$`1P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         0.95         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       23.08        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 
       65.13       110.73        51.35        31.73        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2.04              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            58.19            194.79 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           14.945            25.580 
[1] "2.0 - 58.2 (14.9)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "8.5"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         1        0         6        2
  1P GAIN WILD-TYPE     170       21        46       13
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 1               170
  STAGE II                0                21
  STAGE III               6                46
  STAGE IV                2                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
  1P GAIN MUTATED     2   0     8
  1P GAIN WILD-TYPE 189  33    54
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1                  2               189
  T2                  0                33
  T3+T4               8                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                N0 N1 N2
  1P GAIN MUTATED    0  5  2
  1P GAIN WILD-TYPE 49 19  2
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               0                49
  N1               5                19
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  1
  1P GAIN WILD-TYPE 93  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    1
  1P GAIN WILD-TYPE   93    8
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               1                93
  1               1                 8
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     6   4
  1P GAIN WILD-TYPE  70 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6    4
  1P GAIN WILD-TYPE   70  208
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               6                70
  MALE                 4               208
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                72 
       TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-5P-A9JU        TCGA-B9-A44B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838        TCGA-GL-A59T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-5P-A9K3        TCGA-5P-A9KE        TCGA-A4-8310        TCGA-A4-A48D 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-7268        TCGA-B9-A69E        TCGA-DW-7963 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LE        TCGA-GL-7773 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V10, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                52 
       TCGA-2Z-A9JD        TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-2Z-A9J3        TCGA-2Z-A9J7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0     9
  1P GAIN WILD-TYPE                        61   195
D1V11, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                61
  WHITE                                          9               195
[1] 4 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   9
  1P GAIN WILD-TYPE  12 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    9
  1P GAIN WILD-TYPE   12  231
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               9               231
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED     9   8
  1Q GAIN WILD-TYPE 232  36
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               17               268 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                36 
$`1Q GAIN MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-2Z-A9J2 TCGA-5P-A9K9 TCGA-A4-7287 TCGA-AL-3466 
       12.99        49.25        59.01        19.36        19.63         9.63 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-G7-6789 
       30.28        25.35         7.66         0.95         7.92         4.01 
TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-7130 TCGA-IA-A40Y TCGA-WN-A9G9 
       16.90         3.68        58.19         2.04        26.01 

$`1Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        18.21         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
       10.82         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25        25.22        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        51.35        31.73        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.95              0.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            59.01            194.79 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            16.90             25.74 
[1] "0.9 - 59.0 (16.9)"  "0.1 - 194.8 (25.7)"
[1] "hr=" "6.6"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         3        0        10        3
  1Q GAIN WILD-TYPE     168       21        42       12
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 3               168
  STAGE II                0                21
  STAGE III              10                42
  STAGE IV                3                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 GAIN MUTATED     4   0    13
  1Q GAIN WILD-TYPE 187  33    49
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                  4               187
  T2                  0                33
  T3+T4              13                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                N0 N1 N2
  1Q GAIN MUTATED    4  6  2
  1Q GAIN WILD-TYPE 45 18  2
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0               4                45
  N1               6                18
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    5  2
  1Q GAIN WILD-TYPE 89  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5    2
  1Q GAIN WILD-TYPE   89    7
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               5                89
  1               2                 7
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     9   8
  1Q GAIN WILD-TYPE  67 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      9    8
  1Q GAIN WILD-TYPE   67  204
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               9                67
  MALE                 8               204
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                52 
       TCGA-2Z-A9JD        TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-2Z-A9J3        TCGA-2Z-A9J7 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           0    16
  1Q GAIN WILD-TYPE                        61   188
D2V11, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                61
  WHITE                                         16               188
[1] 4 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     0  15
  1Q GAIN WILD-TYPE  12 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   15
  1Q GAIN WILD-TYPE   12  225
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              15               225
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    34   8
  2P GAIN WILD-TYPE 207  36
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               42               243 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                36 
$`2P GAIN MUTATED`
TCGA-B3-A6W5 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-5561 TCGA-GL-A59T 
       10.16        11.87        11.97        96.92        13.61        17.95 
TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-2Z-A9J5 TCGA-5P-A9K9 TCGA-A4-A4ZT TCGA-A4-A57E 
       84.89        17.75       100.27        19.36        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3466 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 
       16.31        15.75         9.63        49.32         2.20        37.51 
TCGA-B9-4117 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 
        0.46         7.92         2.76        51.19         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NI TCGA-IA-A40U 
       51.78        39.25        23.08         3.68        11.84        16.80 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 
        2.04        18.41        29.10        11.41        34.29        42.94 
TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UZ-A9PK TCGA-V9-A7HT 
       99.12        14.07        28.80        41.62       117.40        31.73 

$`2P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 
       21.86        19.23        26.04        13.25        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       20.12        11.28        48.85       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO 
       67.17        16.34        12.13        29.26        19.73        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        59.01        58.22        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
       19.73        14.33        12.46         8.28        12.46        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
       66.71        62.66        67.73        41.13        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
       12.46        50.50        28.18        26.40        20.61         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 
       25.35        10.82         7.66         0.95       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
        7.17         3.81        40.77        79.86        80.88        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        0.43        90.90        11.05        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        58.19        26.01        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       25.22        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55Z 
       21.34        12.36        12.76        10.55        10.09        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       99.78        87.09         6.61        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL 
       50.60        78.90        47.90        49.45        44.61        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       11.93        19.00        16.31        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       18.02        26.20       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       51.35        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.46              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           117.40            194.79 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           17.355            26.010 
[1] "0.5 - 117.4 (17.4)" "0.1 - 194.8 (26.0)"
[1] "hr=" "1.6"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        24        4         6        6
  2P GAIN WILD-TYPE     147       17        46        9
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                24               147
  STAGE II                4                17
  STAGE III               6                46
  STAGE IV                6                 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
  2P GAIN MUTATED    24   7    11
  2P GAIN WILD-TYPE 167  26    51
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                 24               167
  T2                  7                26
  T3+T4              11                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                N0 N1 N2
  2P GAIN MUTATED    5  7  2
  2P GAIN WILD-TYPE 44 17  2
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0               5                44
  N1               7                17
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   10  5
  2P GAIN WILD-TYPE 84  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     10    5
  2P GAIN WILD-TYPE   84    4
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              10                84
  1               5                 4
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    13  29
  2P GAIN WILD-TYPE  63 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     13   29
  2P GAIN WILD-TYPE   63  183
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              13                63
  MALE                29               183
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     1
  2P GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           8    30
  2P GAIN WILD-TYPE                        53   174
D3V11, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      8                53
  WHITE                                         30               174
[1] 4 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  36
  2P GAIN WILD-TYPE  10 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   36
  2P GAIN WILD-TYPE   10  204
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              36               204
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    38   9
  2Q GAIN WILD-TYPE 203  35
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               47               238 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9                35 
$`2Q GAIN MUTATED`
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-5561 
       21.07        10.16        11.87        11.97        96.92        13.61 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-2Z-A9J5 TCGA-2Z-A9JR TCGA-5P-A9K9 
       17.95        84.89        17.75       100.27         5.29        19.36 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3466 TCGA-AL-3471 
       16.96         8.48        16.31        15.75         9.63        49.32 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B9-4117 TCGA-BQ-5893 TCGA-BQ-5894 
       67.73         2.20        37.51         0.46         7.92         2.76 
TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 
       51.19         1.18         4.01        51.78        39.25        25.84 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD 
       23.08         3.68        11.84        16.80         2.04        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-Q2-A5QZ 
       29.10        11.41        34.29        42.94        99.12        14.07 
TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UZ-A9PK TCGA-UZ-A9PQ TCGA-V9-A7HT 
       28.80        41.62       117.40        86.27        31.73 

$`2Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B9-5155 
       12.99        76.64        49.25        21.67        27.68        21.86 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       19.23        26.04        13.25        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.28        48.85       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-IA-A83W 
       13.78         3.75        14.63         3.02        61.02        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PO 
       16.34        12.13        29.26        19.73        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE 
       86.37        21.60        15.91        15.62         6.74         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       75.55        59.01        58.22        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.46         8.28        12.46        70.19        66.71        62.66 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       26.40        20.61         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        0.95       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       79.86        80.88        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 
       10.68        13.08         2.40         0.43        90.90        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       71.44        25.15        20.52        25.25        17.98        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       56.75        73.25        25.22        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       10.09        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED 
       31.13        15.48        99.78        87.09         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR 
       44.61        27.06        11.93        19.00        16.31        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        18.02        26.20       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        51.35        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.46              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           117.40            194.79 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            17.95             26.01 
[1] "0.5 - 117.4 (17.9)" "0.1 - 194.8 (26.0)"
[1] "hr=" "1.5"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        27        4         7        7
  2Q GAIN WILD-TYPE     144       17        45        8
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                27               144
  STAGE II                4                17
  STAGE III               7                45
  STAGE IV                7                 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
  2Q GAIN MUTATED    27   8    12
  2Q GAIN WILD-TYPE 164  25    50
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                 27               164
  T2                  8                25
  T3+T4              12                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                N0 N1 N2
  2Q GAIN MUTATED    6  8  3
  2Q GAIN WILD-TYPE 43 16  1
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0               6                43
  N1               8                16
  N2               3                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   12  5
  2Q GAIN WILD-TYPE 82  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     12    5
  2Q GAIN WILD-TYPE   82    4
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              12                82
  1               5                 4
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    14  33
  2Q GAIN WILD-TYPE  62 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14   33
  2Q GAIN WILD-TYPE   62  179
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              14                62
  MALE                33               179
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     1
  2Q GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           9    34
  2Q GAIN WILD-TYPE                        52   170
D4V11, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      9                52
  WHITE                                         34               170
[1] 4 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  41
  2Q GAIN WILD-TYPE  10 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   41
  2Q GAIN WILD-TYPE   10  199
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              41               199
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    63  10
  3P GAIN WILD-TYPE 178  34
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               73               212 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                34 
$`3P GAIN MUTATED`
TCGA-AL-3468 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-BQ-5886 TCGA-BQ-7046 
       76.64        21.07        10.16        21.86        26.04        96.92 
TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-GL-A59T TCGA-HE-A5NF 
       48.85        35.93        37.55        24.46        17.95        84.89 
TCGA-PJ-A5Z9 TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-2K-A9WE TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       17.75        21.60        15.91         7.04       100.27        56.91 
TCGA-5P-A9JY TCGA-5P-A9K2 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-A4-7287 TCGA-A4-8311 
       49.58        78.64        19.36        12.99        19.63        23.97 
TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
        0.76        19.73        14.33        12.46        16.96        16.31 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4117 
       49.32         2.20        37.51        30.58        28.18         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-7045 
        1.15        43.99        22.06        17.49        47.80        48.26 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7Q0 TCGA-F9-A7VF 
        7.04         3.81        40.77        51.19        13.08         2.40 
TCGA-G7-6790 TCGA-G7-A8LB TCGA-GL-6846 TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 
       51.78        17.98       194.79        11.21        81.93        58.19 
TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A83S TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       11.84        25.22        85.78        18.41        29.10        11.41 
TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVM TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP 
       87.09         6.61        50.60        28.80        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-UZ-A9Q1 
       41.62        53.10       117.40        71.24        47.47        51.35 
TCGA-V9-A7HT 
       31.73 

$`3P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B9-A44B TCGA-B9-A5W7 
       12.99        49.25        21.67        27.68        11.87        19.23 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       13.25        11.97        44.84        26.27        20.12        11.28 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       13.61       129.86        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       61.02        67.17        16.34        12.13        29.26        19.73 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2Z-A9J1 
       41.33        62.83        86.37        15.62         6.74        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
       59.01        58.22         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
        5.29         0.13        12.82        11.57       106.55        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KC 
       22.26        15.48        71.80        62.93        43.04        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        18.21         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 
       23.28        23.31        19.63         8.48        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 
       29.03        34.49        12.46        50.50        26.40        20.61 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       17.23         0.16        14.86        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        7.92         2.76       123.62        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
       49.84         7.63         7.17        79.86        80.88        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G 
       34.19        19.00        24.89        10.68         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       20.52        25.84        25.25        23.08        16.90        80.65 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
       16.31        26.01        56.75        73.25        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
        2.04        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       12.76        10.55        10.09        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVO 
       42.94        99.12        92.58        52.27        16.01        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM 
       14.07        47.90        49.45        44.61        27.06        11.93 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM 
       26.47        43.76        18.02        26.20       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       37.35        98.96        86.27        30.67        65.13       110.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.46              0.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           194.79            129.86 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           25.220            25.315 
[1] "0.5 - 194.8 (25.2)" "0.1 - 129.9 (25.3)"
[1] "hr=" "1.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED        50        8         6        2
  3P GAIN WILD-TYPE     121       13        46       13
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                50               121
  STAGE II                8                13
  STAGE III               6                46
  STAGE IV                2                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
  3P GAIN MUTATED    54  12     8
  3P GAIN WILD-TYPE 137  21    54
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                 54               137
  T2                 12                21
  T3+T4               8                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                N0 N1 N2
  3P GAIN MUTATED    7  2  1
  3P GAIN WILD-TYPE 42 22  3
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               7                42
  N1               2                22
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   26  0
  3P GAIN WILD-TYPE 68  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26    0
  3P GAIN WILD-TYPE   68    9
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              26                68
  1               0                 9
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    18  57
  3P GAIN WILD-TYPE  58 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     18   57
  3P GAIN WILD-TYPE   58  155
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              18                58
  MALE                57               155
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     1
  3P GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                          13    54
  3P GAIN WILD-TYPE                        48   150
D5V11, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                     13                48
  WHITE                                         54               150
[1] 4 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     3  62
  3P GAIN WILD-TYPE   9 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   62
  3P GAIN WILD-TYPE    9  178
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO              62               178
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    77  16
  3Q GAIN WILD-TYPE 164  28
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               93               192 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16                28 
$`3Q GAIN MUTATED`
TCGA-AL-3468 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-5886 
       76.64        21.07        10.16        21.86        11.87        26.04 
TCGA-BQ-7046 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-GL-A59T TCGA-HE-A5NF 
       96.92        35.93        37.55        24.46        17.95        84.89 
TCGA-IA-A83W TCGA-PJ-A5Z9 TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-2K-A9WE TCGA-2Z-A9J2 
       67.17        17.75        21.60        15.91         7.04        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-5P-A9JY TCGA-5P-A9K2 TCGA-5P-A9K4 
       58.22       100.27        56.91        49.58        78.64        71.80 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-A4-7287 TCGA-A4-7997 TCGA-A4-8311 
       19.36        12.99        12.39        19.63        30.48        23.97 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31         0.76        19.73        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-4103 
       16.31        15.75        49.32         2.20        37.51        30.58 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH 
       28.18         0.46         1.15        43.99        22.06        17.49 
TCGA-BQ-5881 TCGA-BQ-5890 TCGA-BQ-7045 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 
       47.80         7.66        48.26         7.04         3.81        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       80.88        51.19        74.60        34.19        13.08         2.40 
TCGA-G7-6790 TCGA-G7-A8LB TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A9DD TCGA-HE-7129 
       51.78        17.98        16.90       194.79        11.21        81.93 
TCGA-HE-7130 TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A83S TCGA-KV-A6GD TCGA-KV-A6GE 
       58.19        11.84        25.22        85.78        18.41        29.10 
TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-P4-AAVM 
       11.41        99.78        87.09         6.61        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS 
       14.07        28.80        19.00        16.31        41.62        53.10 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      117.40       125.29        37.35        71.24        30.67        47.47 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
      110.73        51.35        31.73 

$`3Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B9-A5W7 TCGA-BQ-5888 
       12.99        49.25        21.67        27.68        19.23        13.25 
TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       11.97        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       13.61       129.86        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO 
       61.02        16.34        12.13        29.26        19.73        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2Z-A9J1 TCGA-2Z-A9J7 
       62.83        86.37        15.62         6.74        75.55         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K6 
       11.57       106.55        90.21        22.26        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 
       43.04        27.09        67.43        18.21         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 
       19.13         7.82         0.23        16.64        29.46        25.64 
TCGA-A4-8312 TCGA-A4-8517 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
       23.28        19.63         8.48         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47N 
       70.19        66.71        62.66        67.73        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 
       20.25        16.77        20.32        33.83        29.03        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A5W9 
       12.46        50.50        26.40        20.61        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       25.35        10.82         0.95         7.92         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 
       93.34        61.28        50.40        49.84         7.63         7.17 
TCGA-DZ-6131 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G 
       79.86        19.00        24.89        10.68         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 
       20.52        25.84        25.25        23.08        80.65        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE 
        3.68        27.65         1.05        12.43        12.89        16.31 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       26.01        56.75        73.25        16.80        19.99         2.04 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       10.55        10.09        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E8 TCGA-P4-A5EB 
       20.25        17.62        31.13        15.48        42.94        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       92.58        52.27        78.90        47.90        49.45        44.61 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       27.06        11.93        26.47        43.76        18.02        26.20 
TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PX TCGA-WN-A9G9 TCGA-WN-AB4C 
      103.63        98.96        86.27        65.13        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.46              0.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           194.79            129.86 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            28.18             25.20 
[1] "0.5 - 194.8 (28.2)" "0.1 - 129.9 (25.2)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        58       11        13        2
  3Q GAIN WILD-TYPE     113       10        39       13
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                58               113
  STAGE II               11                10
  STAGE III              13                39
  STAGE IV                2                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    65  15    14
  3Q GAIN WILD-TYPE 126  18    48
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                 65               126
  T2                 15                18
  T3+T4              14                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  3Q GAIN MUTATED   11  4  1
  3Q GAIN WILD-TYPE 38 20  3
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              11                38
  N1               4                20
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   29  0
  3Q GAIN WILD-TYPE 65  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     29    0
  3Q GAIN WILD-TYPE   65    9
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              29                65
  1               0                 9
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    22  73
  3Q GAIN WILD-TYPE  54 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     22   73
  3Q GAIN WILD-TYPE   54  139
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              22                54
  MALE                73               139
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  2     1
  3Q GAIN WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          16    68
  3Q GAIN WILD-TYPE                        45   136
D6V11, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                     16                45
  WHITE                                         68               136
[1] 4 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     4  78
  3Q GAIN WILD-TYPE   8 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4   78
  3Q GAIN WILD-TYPE    8  162
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO              78               162
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     8   2
  4P GAIN WILD-TYPE 233  42
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               275 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                42 
$`4P GAIN MUTATED`
TCGA-BQ-5892 TCGA-UZ-A9PO TCGA-AL-3466 TCGA-B9-4114 TCGA-B9-A5W9 TCGA-G7-6789 
       11.97        62.83         9.63        28.18         0.16         4.01 
TCGA-G7-6795 TCGA-G7-A8LC TCGA-SX-A7SR TCGA-WN-AB4C 
       39.25        23.08        26.47        39.06 

$`4P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       41.33        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
        8.48        16.31        15.75         8.28        12.46        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 
       29.03        30.58        34.49        12.46        50.50        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
        0.43        51.78        90.90        11.05        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       20.52        25.84        25.25        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS 
       27.06        11.93        19.00        16.31        41.62        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A894 
       65.13       110.73        51.35        31.73        26.01        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.16              0.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            62.83            194.79 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           24.775            25.280 
[1] "0.2 - 62.8 (24.8)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "2"  
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         6        1         0        2
  4P GAIN WILD-TYPE     165       20        52       13
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 6               165
  STAGE II                1                20
  STAGE III               0                52
  STAGE IV                2                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 GAIN MUTATED     6   2     2
  4P GAIN WILD-TYPE 185  31    60
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                  6               185
  T2                  2                31
  T3+T4               2                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                N0 N1 N2
  4P GAIN MUTATED    2  1  1
  4P GAIN WILD-TYPE 47 23  3
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               2                47
  N1               1                23
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 92  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   92    8
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               2                92
  1               1                 8
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2   8
  4P GAIN WILD-TYPE  74 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    8
  4P GAIN WILD-TYPE   74  204
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                74
  MALE                 8               204
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1     9
  4P GAIN WILD-TYPE                        60   195
D7V11, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                60
  WHITE                                          9               195
[1] 4 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     0  10
  4P GAIN WILD-TYPE  12 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   10
  4P GAIN WILD-TYPE   12  230
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              10               230
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     8   1
  4Q GAIN WILD-TYPE 233  43
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               276 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                43 
$`4Q GAIN MUTATED`
TCGA-BQ-5892 TCGA-UZ-A9PO TCGA-B9-4114 TCGA-B9-A5W9 TCGA-G7-6789 TCGA-G7-6795 
       11.97        62.83        28.18         0.16         4.01        39.25 
TCGA-G7-A8LC TCGA-SX-A7SR TCGA-WN-AB4C 
       23.08        26.47        39.06 

$`4Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       41.33        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       17.23        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
        1.18         0.43        51.78        90.90        11.05        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       25.15        20.52        25.84        25.25        17.98        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.16              0.10 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            62.83            194.79 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           26.470            25.265 
[1] "0.2 - 62.8 (26.5)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "1"  
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         6        1         0        1
  4Q GAIN WILD-TYPE     165       20        52       14
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 6               165
  STAGE II                1                20
  STAGE III               0                52
  STAGE IV                1                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
  4Q GAIN MUTATED     6   2     1
  4Q GAIN WILD-TYPE 185  31    61
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                  6               185
  T2                  2                31
  T3+T4               1                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"
                   vv
clus                N0 N1 N2
  4Q GAIN MUTATED    2  0  1
  4Q GAIN WILD-TYPE 47 24  3
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               2                47
  N1               0                24
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    2  0
  4Q GAIN WILD-TYPE 92  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    0
  4Q GAIN WILD-TYPE   92    9
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               2                92
  1               0                 9
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2   7
  4Q GAIN WILD-TYPE  74 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    7
  4Q GAIN WILD-TYPE   74  205
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                74
  MALE                 7               205
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           1     8
  4Q GAIN WILD-TYPE                        60   196
D8V11, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                60
  WHITE                                          8               196
[1] 4 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     0   9
  4Q GAIN WILD-TYPE  12 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    9
  4Q GAIN WILD-TYPE   12  231
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               9               231
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    26   7
  5P GAIN WILD-TYPE 215  37
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               33               252 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                37 
$`5P GAIN MUTATED`
TCGA-BQ-5892 TCGA-DW-7838 TCGA-2K-A9WE TCGA-2Z-A9J3 TCGA-4A-A93X TCGA-5P-A9K9 
       11.97        24.46         7.04        58.22        12.82        19.36 
TCGA-A4-7287 TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3466 
       19.63        29.46         0.76        12.46         8.48         9.63 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 
       62.66        41.13        20.32         0.46         0.16        25.35 
TCGA-BQ-5891 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-A8LC 
        0.95        79.86        19.00        13.08         4.01        23.08 
TCGA-GL-A4EM TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5EB 
        1.05        58.19        73.25         2.04        18.41        99.12 
TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A7SQ 
       16.01        14.07        41.62 

$`5P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       75.55        59.01       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       18.21         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.63        19.73        14.33        16.96        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
        8.28        12.46        70.19        49.32        66.71        67.73 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 
        2.20        37.51        36.49        20.25        16.77        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       26.40        20.61         1.15        43.99        22.06        17.23 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 
       26.04        30.28        10.82         7.66         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 
        7.63         7.04         7.17         3.81        40.77        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       51.19        74.60        34.19        24.89        10.68         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       11.84        56.75        25.22        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.55        10.09        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09        42.94         6.61        92.58        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        11.93        19.00        16.31        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.16              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            99.12            194.79 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            18.41             26.04 
[1] "0.2 - 99.1 (18.4)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "2.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED        15        3         9        4
  5P GAIN WILD-TYPE     156       18        43       11
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                15               156
  STAGE II                3                18
  STAGE III               9                43
  STAGE IV                4                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
  5P GAIN MUTATED    16   5    13
  5P GAIN WILD-TYPE 175  28    49
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                 16               175
  T2                  5                28
  T3+T4              13                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                N0 N1 N2
  5P GAIN MUTATED    9  3  2
  5P GAIN WILD-TYPE 40 21  2
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0               9                40
  N1               3                21
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   13  2
  5P GAIN WILD-TYPE 81  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     13    2
  5P GAIN WILD-TYPE   81    7
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              13                81
  1               2                 7
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     9  25
  5P GAIN WILD-TYPE  67 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9   25
  5P GAIN WILD-TYPE   67  187
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               9                67
  MALE                25               187
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     1
  5P GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           4    26
  5P GAIN WILD-TYPE                        57   178
D9V11, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      4                57
  WHITE                                         26               178
[1] 4 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     1  27
  5P GAIN WILD-TYPE  11 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   27
  5P GAIN WILD-TYPE   11  213
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              27               213
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    26   4
  5Q GAIN WILD-TYPE 215  40
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               30               255 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                40 
$`5Q GAIN MUTATED`
TCGA-BQ-5892 TCGA-DW-7838 TCGA-2K-A9WE TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-8098 
       11.97        24.46         7.04        12.82        19.36        29.46 
TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 
        0.76        12.46         8.48         9.63        62.66        41.13 
TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-EV-5902 
       20.32         0.46         0.16        25.35         0.95        19.00 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-7130 TCGA-HE-A5NK 
       13.08         4.01        23.08         1.05        58.19        73.25 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
        2.04        18.41        99.78        99.12        14.07        41.62 

$`5Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
        7.82         0.23        16.64        30.48        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.28        23.31        19.63        19.73        14.33        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
       16.31        15.75         8.28        12.46        70.19        49.32 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       66.71        67.73         2.20        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       16.77        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       22.06        17.23        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 
       21.63        40.83        26.04        30.28        10.82         7.66 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       24.89        10.68         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92         3.68        27.65        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       16.31        81.93        26.01        11.84        56.75        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GE 
       21.34        12.36        12.76        10.55        10.09        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       17.62        31.13        15.48        87.09        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       16.31        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.16              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            99.78            194.79 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            16.24             26.04 
[1] "0.2 - 99.8 (16.2)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED        14        2         8        4
  5Q GAIN WILD-TYPE     157       19        44       11
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                14               157
  STAGE II                2                19
  STAGE III               8                44
  STAGE IV                4                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
  5Q GAIN MUTATED    16   4    11
  5Q GAIN WILD-TYPE 175  29    51
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                 16               175
  T2                  4                29
  T3+T4              11                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                N0 N1 N2
  5Q GAIN MUTATED    7  4  2
  5Q GAIN WILD-TYPE 42 20  2
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               7                42
  N1               4                20
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   13  2
  5Q GAIN WILD-TYPE 81  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     13    2
  5Q GAIN WILD-TYPE   81    7
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              13                81
  1               2                 7
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     8  23
  5Q GAIN WILD-TYPE  68 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8   23
  5Q GAIN WILD-TYPE   68  189
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               8                68
  MALE                23               189
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           5    22
  5Q GAIN WILD-TYPE                        56   182
D10V11, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      5                56
  WHITE                                         22               182
[1] 4 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     0  26
  5Q GAIN WILD-TYPE  12 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   26
  5Q GAIN WILD-TYPE   12  214
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              26               214
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     5   5
  6P GAIN WILD-TYPE 236  39
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               275 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5                39 
$`6P GAIN MUTATED`
TCGA-AL-A5DJ TCGA-DW-5561 TCGA-4A-A93X TCGA-AL-3466 TCGA-B9-A69E TCGA-BQ-5893 
       49.25        13.61        12.82         9.63        14.86         7.92 
TCGA-BQ-7048 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
       93.34         6.61        14.07        86.27 

$`6P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
       16.31        15.75         8.28        12.46        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        2.76       123.62        48.26        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       78.90        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             6.61              0.10 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            93.34            194.79 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            13.84             25.58 
[1] "6.6 - 93.3 (13.8)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "4.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         1        0         6        3
  6P GAIN WILD-TYPE     170       21        46       12
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 1               170
  STAGE II                0                21
  STAGE III               6                46
  STAGE IV                3                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
  6P GAIN MUTATED     1   1     8
  6P GAIN WILD-TYPE 190  32    54
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                  1               190
  T2                  1                32
  T3+T4               8                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                N0 N1 N2
  6P GAIN MUTATED    1  5  0
  6P GAIN WILD-TYPE 48 19  4
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               1                48
  N1               5                19
  N2               0                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    2  2
  6P GAIN WILD-TYPE 92  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    2
  6P GAIN WILD-TYPE   92    7
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               2                92
  1               2                 7
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3   7
  6P GAIN WILD-TYPE  73 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    7
  6P GAIN WILD-TYPE   73  205
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               3                73
  MALE                 7               205
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
D11V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           3     7
  6P GAIN WILD-TYPE                        58   197
D11V11, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      3                58
  WHITE                                          7               197
[1] 4 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     0  10
  6P GAIN WILD-TYPE  12 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   10
  6P GAIN WILD-TYPE   12  230
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              10               230
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     3   4
  6Q GAIN WILD-TYPE 238  40
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                7               278 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                40 
$`6Q GAIN MUTATED`
TCGA-AL-A5DJ TCGA-DW-5561 TCGA-4A-A93X TCGA-AL-3466 TCGA-BQ-5893 TCGA-P4-A5EA 
       49.25        13.61        12.82         9.63         7.92         6.61 
TCGA-Q2-A5QZ 
       14.07 

$`6Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
       16.31        15.75         8.28        12.46        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        0.95         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09        42.94        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             6.61              0.10 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            49.25            194.79 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            12.82             25.61 
[1] "6.6 - 49.2 (12.8)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "11" 
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         1        0         3        3
  6Q GAIN WILD-TYPE     170       21        49       12
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 1               170
  STAGE II                0                21
  STAGE III               3                49
  STAGE IV                3                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
  6Q GAIN MUTATED     1   0     6
  6Q GAIN WILD-TYPE 190  33    56
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1                  1               190
  T2                  0                33
  T3+T4               6                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"
                   vv
clus                N0 N1 N2
  6Q GAIN MUTATED    0  4  0
  6Q GAIN WILD-TYPE 49 20  4
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0               0                49
  N1               4                20
  N2               0                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  2
  6Q GAIN WILD-TYPE 93  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    2
  6Q GAIN WILD-TYPE   93    7
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               1                93
  1               2                 7
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3   4
  6Q GAIN WILD-TYPE  73 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    4
  6Q GAIN WILD-TYPE   73  208
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                73
  MALE                 4               208
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                52 
       TCGA-2Z-A9JD        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-SX-A71S        TCGA-SX-A71U 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     0
  6Q GAIN WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           2     5
  6Q GAIN WILD-TYPE                        59   199
D12V11, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      2                59
  WHITE                                          5               199
[1] 4 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     0   7
  6Q GAIN WILD-TYPE  12 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    7
  6Q GAIN WILD-TYPE   12  233
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               7               233
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   146  22
  7P GAIN WILD-TYPE  95  22
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              168               117 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               22                22 
$`7P GAIN MUTATED`
TCGA-2Z-A9JD TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 
       34.85        25.58        16.18        22.49        12.26        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A657 
       21.37         0.89        76.64        49.25        21.67        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-5561 
       10.16        21.86        19.23        96.92        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 
      129.86        35.93        37.55        24.46         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-PJ-A5Z9 
        3.02        61.02        17.95        84.89        16.34        17.75 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-2K-A9WE 
       62.83        86.37        21.60        15.91        15.62         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE 
       75.55        58.22       100.27        56.91         4.57        56.81 
TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JY 
       30.71        29.36         5.29         0.13        12.82        49.58 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KC 
       22.26        78.64        71.80        62.93        19.36        12.39 
TCGA-5P-A9KE TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
       27.09        19.13        16.64        30.48        25.64        23.97 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E 
       23.31         0.76        19.63        14.33        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
       16.31        15.75        12.46        49.32        66.71        67.73 
TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
        2.20        36.49        20.25        20.32        33.83        30.58 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       12.46        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 
       43.99        22.06        17.49        47.80        26.04        25.35 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7051 
       10.82         0.95         2.76       123.62        48.26        50.40 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 
        7.63         7.04         7.17         3.81        40.77        80.88 
TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       51.19        34.19        24.89        13.08         2.40         1.18 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        4.01        51.78        39.25        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R 
       23.08        80.65       194.79         3.68        27.65        12.43 
TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 
       25.22         2.04        88.24        96.69        21.34        12.36 
TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK TCGA-P4-AAVL TCGA-Q2-A5QZ 
       20.25        15.48        87.09        52.27        16.01        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        49.45        44.61        28.80        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
      117.40       125.29        37.35        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8S0 
      110.73        51.35        31.73        18.64        25.28         6.02 

$`7P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-B1-A47O 
       75.42        39.88        33.07        67.17        12.99        27.68 
TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 
       11.87        26.04        13.25        11.97        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 TCGA-IA-A83W TCGA-MH-A855 TCGA-MH-A857 
       20.12        11.28        13.78        67.17        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JG 
       19.73        41.33         6.74        59.01        91.73        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-5P-A9JW 
       51.52        38.99        24.33        31.20        11.57       106.55 
TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KH TCGA-A4-7286 
       90.21        15.48        43.04        12.99        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 
       19.63         0.10        35.18         7.82         0.23        29.46 
TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 
       23.28        19.73        12.46         8.28         9.63        70.19 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 
       62.66        41.13        37.51        16.77        29.03        34.49 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
       20.61        17.23         0.16        14.86        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 
       19.27         8.88        63.72        22.92        43.20        21.63 
TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7050 
       40.83        30.28         7.66         7.92        93.34        61.28 
TCGA-BQ-7053 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G 
       49.84        79.86        74.60        19.00        10.68         0.43 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD 
       90.90        11.05        71.44        25.15        20.52        16.90 
TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U 
       12.92         1.05        12.89        16.31        73.25        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IZ-8195 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A560 
       19.99        85.78        22.26        10.55        10.09        30.38 
TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        17.62        31.13        99.78        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A7SL TCGA-UN-AAZ9 
       99.12        92.58        50.60        78.90        27.06        18.02 
TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C 
      103.63        98.96        86.27        71.24        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8S1 
       18.64        18.05        13.28 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.13              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           194.79            106.55 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           25.265            26.010 
[1] "0.1 - 194.8 (25.3)" "0.1 - 106.5 (26.0)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED       111       11        21       11
  7P GAIN WILD-TYPE      60       10        31        4
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I               111                60
  STAGE II               11                10
  STAGE III              21                31
  STAGE IV               11                 4
[1] 4 2
[1] 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   121  19    30
  7P GAIN WILD-TYPE  70  14    32
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                121                70
  T2                 19                14
  T3+T4              30                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                N0 N1 N2
  7P GAIN MUTATED   23 10  3
  7P GAIN WILD-TYPE 26 14  1
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              23                26
  N1              10                14
  N2               3                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   51  6
  7P GAIN WILD-TYPE 43  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     51    6
  7P GAIN WILD-TYPE   43    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              51                43
  1               6                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    34 137
  7P GAIN WILD-TYPE  42  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     34  137
  7P GAIN WILD-TYPE   42   75
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              34                42
  MALE               137                75
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  2     3
  7P GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          30   125
  7P GAIN WILD-TYPE                        31    79
D13V11, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                     30                31
  WHITE                                        125                79
[1] 4 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     6 147
  7P GAIN WILD-TYPE   6  93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6  147
  7P GAIN WILD-TYPE    6   93
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 6
  NOT HISPANIC OR LATINO             147                93
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   147  22
  7Q GAIN WILD-TYPE  94  22
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              169               116 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22                22 
$`7Q GAIN MUTATED`
TCGA-2Z-A9JD TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 
       34.85        25.58        16.18        22.49        12.26        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A657 
       21.37         0.89        76.64        49.25        21.67        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-5560 
       10.16        21.86        19.23        11.97        96.92        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        24.46         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 
       14.63         3.02        61.02        17.95        84.89        16.34 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       17.75        62.83        86.37        21.60        15.91        15.62 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        58.22       100.27        56.91         4.57 
TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       56.81        30.71        29.36         5.29         0.13        12.82 
TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 
       49.58        22.26        78.64        71.80        62.93        19.36 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
       12.39        27.09        19.13        16.64        30.48        25.64 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.97        23.31         0.76        19.63        14.33        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 TCGA-AL-3472 
        8.48        16.31        15.75        12.46        49.32        66.71 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 
       67.73         2.20        36.49        20.25        20.32        33.83 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       30.58        12.46        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 
        1.15        43.99        22.06        17.49        47.80        26.04 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       25.35        10.82         0.95         2.76       123.62        48.26 
TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       50.40         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       80.88        51.19        34.19        24.89        13.08         2.40 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM 
        1.18         4.01        51.78        39.25        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       17.98        23.08        80.65       194.79         3.68        27.65 
TCGA-GL-A59R TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.43        11.21        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 
       56.75        25.22         2.04        88.24        96.69        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36        12.76        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK TCGA-P4-AAVL 
       27.78        20.25        15.48        87.09        52.27        16.01 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
       14.07        47.90        49.45        44.61        28.80        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PU TCGA-UZ-A9PV 
       26.20       117.40       125.29        37.35        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A896 TCGA-Y8-A8RY 
       65.13       110.73        51.35        31.73        18.64        25.28 
TCGA-Y8-A8S0 
        6.02 

$`7Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-B1-A47O 
       75.42        39.88        33.07        67.17        12.99        27.68 
TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       11.87        26.04        13.25        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-7839 TCGA-IA-A83W TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       11.28        13.78        67.17        12.13        29.26        19.73 
TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       41.33         6.74        59.01        91.73        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
       38.99        24.33        31.20        11.57       106.55        90.21 
TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       15.48        43.04        12.99        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 
        0.10        35.18         7.82         0.23        29.46        23.28 
TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 
       19.73        12.46         8.28         9.63        70.19        62.66 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 
       41.13        37.51        16.77        29.03        34.49        20.61 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       17.23         0.16        14.86        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        21.63        40.83 
TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 
       30.28         7.66         7.92        93.34        61.28        49.84 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 
       79.86        74.60        19.00        10.68         0.43        90.90 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 
       11.05        71.44        25.15        20.52        16.90        12.92 
TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
        1.05        12.89        16.31        73.25        16.80        19.99 
TCGA-IA-A83S TCGA-IZ-8195 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A560 TCGA-MH-A561 
       85.78        22.26        10.55        10.09        30.38        27.65 
TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       17.62        31.13        99.78        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PL 
       92.58        50.60        78.90        27.06        18.02       103.63 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       98.96        86.27        71.24        26.01        39.06        18.64 
TCGA-Y8-A897 TCGA-Y8-A8S1 
       18.05        13.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.13              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           194.79            106.55 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           25.250            26.025 
[1] "0.1 - 194.8 (25.2)" "0.1 - 106.5 (26.0)"
[1] "hr=" "1.3"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED       112       11        21       11
  7Q GAIN WILD-TYPE      59       10        31        4
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I               112                59
  STAGE II               11                10
  STAGE III              21                31
  STAGE IV               11                 4
[1] 4 2
[1] 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   122  19    30
  7Q GAIN WILD-TYPE  69  14    32
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                122                69
  T2                 19                14
  T3+T4              30                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                N0 N1 N2
  7Q GAIN MUTATED   24 10  3
  7Q GAIN WILD-TYPE 25 14  1
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              24                25
  N1              10                14
  N2               3                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   52  6
  7Q GAIN WILD-TYPE 42  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     52    6
  7Q GAIN WILD-TYPE   42    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              52                42
  1               6                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    34 138
  7Q GAIN WILD-TYPE  42  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     34  138
  7Q GAIN WILD-TYPE   42   74
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              34                42
  MALE               138                74
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  2     3
  7Q GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          30   126
  7Q GAIN WILD-TYPE                        31    78
D14V11, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                     30                31
  WHITE                                        126                78
[1] 4 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     6 148
  7Q GAIN WILD-TYPE   6  92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6  148
  7Q GAIN WILD-TYPE    6   92
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 6
  NOT HISPANIC OR LATINO             148                92
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    14   6
  8P GAIN WILD-TYPE 227  38
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               20               265 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                38 
$`8P GAIN MUTATED`
TCGA-B1-A47O TCGA-BQ-7056 TCGA-2Z-A9J2 TCGA-2Z-A9JP TCGA-4A-A93X TCGA-5P-A9K9 
       27.68        20.12        59.01        29.36        12.82        19.36 
TCGA-A4-8630 TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-G7-6789 
       14.33        49.32         0.16        43.20        25.35         4.01 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-SX-A71U 
        3.68         1.05        22.26         6.61        16.01        44.61 
TCGA-SX-A7SR TCGA-V9-A7HT 
       26.47        31.73 

$`8P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        49.25        21.67        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       96.92        44.84        26.27        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       24.33        31.20         5.29         0.13        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D 
       23.28        23.31         0.76        19.63        19.73        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       22.06        17.23        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27         8.88        63.72        22.92        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       40.83        26.04        30.28        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R 
       16.90        80.65       194.79        12.92        27.65        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 
        2.04        85.78        88.24        96.69        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       31.13        15.48        99.78        87.09        42.94        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       92.58        52.27        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       49.45        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 
       30.67        47.47        65.13       110.73        51.35        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.16              0.10 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            59.01            194.79 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            21.19             25.58 
[1] "0.2 - 59.0 (21.2)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "3.6"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         8        3         6        2
  8P GAIN WILD-TYPE     163       18        46       13
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 8               163
  STAGE II                3                18
  STAGE III               6                46
  STAGE IV                2                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     8   3     9
  8P GAIN WILD-TYPE 183  30    53
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  8               183
  T2                  3                30
  T3+T4               9                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                N0 N1 N2
  8P GAIN MUTATED    4  4  2
  8P GAIN WILD-TYPE 45 20  2
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0               4                45
  N1               4                20
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    6  0
  8P GAIN WILD-TYPE 88  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      6    0
  8P GAIN WILD-TYPE   88    9
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               6                88
  1               0                 9
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     8  12
  8P GAIN WILD-TYPE  68 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      8   12
  8P GAIN WILD-TYPE   68  200
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               8                68
  MALE                12               200
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                52 
       TCGA-2Z-A9JD        TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-2Z-A9J3        TCGA-2Z-A9J7 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-Q2-A5QZ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           1    19
  8P GAIN WILD-TYPE                        60   185
D15V11, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                60
  WHITE                                         19               185
[1] 4 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     1  17
  8P GAIN WILD-TYPE  11 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   17
  8P GAIN WILD-TYPE   11  223
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              17               223
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    16   9
  8Q GAIN WILD-TYPE 225  35
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               25               260 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                35 
$`8Q GAIN MUTATED`
TCGA-BQ-7056 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9JP TCGA-4A-A93X TCGA-5P-A9K9 
       20.12        59.01        58.22        29.36        12.82        19.36 
TCGA-A4-8630 TCGA-AL-3466 TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 
       14.33         9.63        49.32         0.16        43.20        25.35 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y 
        1.18         4.01        11.05         3.68         1.05         2.04 
TCGA-IZ-8195 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71U TCGA-SX-A7SR 
       22.26         6.61        16.01        14.07        44.61        26.47 
TCGA-V9-A7HT 
       31.73 

$`8Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-DW-5560 
       11.97        96.92        44.84        26.27        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        6.74         7.04        75.55       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       24.33        31.20         5.29         0.13        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D 
       23.28        23.31         0.76        19.63        19.73        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       17.23        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        30.28        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 
       24.89        10.68        13.08         2.40         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       90.90        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       12.92        27.65        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94        99.12        92.58        52.27        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        49.45        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       16.31        41.62        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.16              0.10 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            59.01            194.79 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           16.010            25.925 
[1] "0.2 - 59.0 (16.0)"  "0.1 - 194.8 (25.9)"
[1] "hr=" "5.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         7        4         8        5
  8Q GAIN WILD-TYPE     164       17        44       10
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 7               164
  STAGE II                4                17
  STAGE III               8                44
  STAGE IV                5                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
  8Q GAIN MUTATED     7   4    14
  8Q GAIN WILD-TYPE 184  29    48
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  7               184
  T2                  4                29
  T3+T4              14                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  8Q GAIN MUTATED    3  7  3
  8Q GAIN WILD-TYPE 46 17  1
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0               3                46
  N1               7                17
  N2               3                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6  2
  8Q GAIN WILD-TYPE 88  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    2
  8Q GAIN WILD-TYPE   88    7
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               6                88
  1               2                 7
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    11  14
  8Q GAIN WILD-TYPE  65 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     11   14
  8Q GAIN WILD-TYPE   65  198
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              11                65
  MALE                14               198
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     1
  8Q GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           2    22
  8Q GAIN WILD-TYPE                        59   182
D16V11, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      2                59
  WHITE                                         22               182
[1] 4 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     1  22
  8Q GAIN WILD-TYPE  11 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   22
  8Q GAIN WILD-TYPE   11  218
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              22               218
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     2   1
  9P GAIN WILD-TYPE 239  43
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               282 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                43 
$`9P GAIN MUTATED`
TCGA-BQ-7058 TCGA-B3-4104 TCGA-GL-7966 
       11.28        34.49         3.68 

$`9P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 
       11.97        96.92        44.84        26.27        20.12        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        29.03        30.58        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
      194.79        12.92        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             3.68              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            34.49            194.79 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           11.280            25.315 
[1] "3.7 - 34.5 (11.3)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "5.9"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         0        1         2        0
  9P GAIN WILD-TYPE     171       20        50       15
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0               171
  STAGE II                1                20
  STAGE III               2                50
  STAGE IV                0                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
  9P GAIN MUTATED     0   1     2
  9P GAIN WILD-TYPE 191  32    60
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1                  0               191
  T2                  1                32
  T3+T4               2                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                N0 N1 N2
  9P GAIN MUTATED    0  1  0
  9P GAIN WILD-TYPE 49 23  4
D17V5, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                76 
       TCGA-5P-A9JU        TCGA-A4-A5Y1        TCGA-B1-A47O        TCGA-B1-A657 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5892        TCGA-BQ-7056        TCGA-IA-A83W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-2Z-A9J1        TCGA-2Z-A9JO        TCGA-4A-A93W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-5P-A9K9        TCGA-A4-7583 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E        TCGA-A4-A7UZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656        TCGA-B9-7268 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5889 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5893        TCGA-BQ-5894 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-F9-A8NY        TCGA-F9-A97G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-GL-6846        TCGA-GL-A59R        TCGA-GL-A9DC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720        TCGA-J7-8537 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J7-A8I2        TCGA-KV-A74V        TCGA-P4-A5E6        TCGA-P4-A5E8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-P4-A5EA        TCGA-P4-AAVK        TCGA-P4-AAVL        TCGA-SX-A71R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SP        TCGA-SX-A7SS        TCGA-UN-AAZ9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PQ        TCGA-UZ-A9PX        TCGA-Y8-A897 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D17V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  0
  9P GAIN WILD-TYPE 92  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    0
  9P GAIN WILD-TYPE   92    9
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               2                92
  1               0                 9
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1   2
  9P GAIN WILD-TYPE  75 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    2
  9P GAIN WILD-TYPE   75  210
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               1                75
  MALE                 2               210
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0     3
  9P GAIN WILD-TYPE                        61   201
D17V11, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                61
  WHITE                                          3               201
[1] 4 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     0   3
  9P GAIN WILD-TYPE  12 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    3
  9P GAIN WILD-TYPE   12  237
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               3               237
[1] 2 2
[1] FALSE

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     6   2
  10P GAIN WILD-TYPE 235  42
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                277 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 42 
$`10P GAIN MUTATED`
TCGA-AL-3468 TCGA-5P-A9K9 TCGA-A4-8098 TCGA-B9-4617 TCGA-F9-A7Q0 TCGA-F9-A8NY 
       76.64        19.36        29.46         1.15        13.08         1.18 
TCGA-HE-7130 TCGA-SX-A7SS 
       58.19        53.10 

$`10P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       30.48        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       26.40        20.61         0.46        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G 
       34.19        19.00        24.89        10.68         2.40         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.15               0.10 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             76.64             194.79 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             24.41              25.28 
[1] "1.1 - 76.6 (24.4)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "1.8"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         3        1         1        1
  10P GAIN WILD-TYPE     168       20        51       14
D18V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  3                168
  STAGE II                 1                 20
  STAGE III                1                 51
  STAGE IV                 1                 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 GAIN MUTATED     4   1     3
  10P GAIN WILD-TYPE 187  32    59
D18V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                   4                187
  T2                   1                 32
  T3+T4                3                 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                 N0 N1 N2
  10P GAIN MUTATED    1  1  1
  10P GAIN WILD-TYPE 48 23  3
D18V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                1                 48
  N1                1                 23
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    5  1
  10P GAIN WILD-TYPE 89  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    1
  10P GAIN WILD-TYPE   89    8
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                5                 89
  1                1                  8
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4   4
  10P GAIN WILD-TYPE  72 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    4
  10P GAIN WILD-TYPE   72  208
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                4                 72
  MALE                  4                208
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 73 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         TCGA-2Z-A9JN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-5P-A9K3         TCGA-5P-A9KE         TCGA-A4-8310 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4114         TCGA-B9-4115 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-7268         TCGA-B9-A69E 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6792 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IA-A83V         TCGA-MH-A854 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E7         TCGA-P4-A5EB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A8RY 
"10P GAIN WILD-TYPE" 
D18V10, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 53 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6793         TCGA-G7-6795 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-IA-A40U         TCGA-MH-A854 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E6         TCGA-P4-AAVK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     2
  10P GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2     3
  10P GAIN WILD-TYPE                        59   201
D18V11, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       2                 59
  WHITE                                           3                201
[1] 4 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
  10P GAIN MUTATED     0   7
  10P GAIN WILD-TYPE  12 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    7
  10P GAIN WILD-TYPE   12  233
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                7                233
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     6   2
  10Q GAIN WILD-TYPE 235  42
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                277 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 42 
$`10Q GAIN MUTATED`
TCGA-AL-3468 TCGA-5P-A9K9 TCGA-A4-8098 TCGA-B9-4617 TCGA-F9-A7Q0 TCGA-F9-A8NY 
       76.64        19.36        29.46         1.15        13.08         1.18 
TCGA-HE-7130 TCGA-SX-A7SS 
       58.19        53.10 

$`10Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       30.48        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       26.40        20.61         0.46        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G 
       34.19        19.00        24.89        10.68         2.40         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.15               0.10 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             76.64             194.79 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             24.41              25.28 
[1] "1.1 - 76.6 (24.4)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "1.8"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         3        1         1        1
  10Q GAIN WILD-TYPE     168       20        51       14
D19V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  3                168
  STAGE II                 1                 20
  STAGE III                1                 51
  STAGE IV                 1                 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
  10Q GAIN MUTATED     4   1     3
  10Q GAIN WILD-TYPE 187  32    59
D19V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                   4                187
  T2                   1                 32
  T3+T4                3                 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                 N0 N1 N2
  10Q GAIN MUTATED    1  1  1
  10Q GAIN WILD-TYPE 48 23  3
D19V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                1                 48
  N1                1                 23
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    5  1
  10Q GAIN WILD-TYPE 89  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    1
  10Q GAIN WILD-TYPE   89    8
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                5                 89
  1                1                  8
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     4   4
  10Q GAIN WILD-TYPE  72 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4    4
  10Q GAIN WILD-TYPE   72  208
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                4                 72
  MALE                  4                208
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 73 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         TCGA-2Z-A9JN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-5P-A9K3         TCGA-5P-A9KE         TCGA-A4-8310 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4114         TCGA-B9-4115 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-7268         TCGA-B9-A69E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6792 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IA-A83V         TCGA-MH-A854 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E7         TCGA-P4-A5EB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY 
"10Q GAIN WILD-TYPE" 
D19V10, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 53 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6793         TCGA-G7-6795 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-IA-A40U         TCGA-MH-A854 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E6         TCGA-P4-AAVK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           2     3
  10Q GAIN WILD-TYPE                        59   201
D19V11, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       2                 59
  WHITE                                           3                201
[1] 4 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
  10Q GAIN MUTATED     0   7
  10Q GAIN WILD-TYPE  12 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    7
  10Q GAIN WILD-TYPE   12  233
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                7                233
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     7   4
  11P GAIN WILD-TYPE 234  40
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                274 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 40 
$`11P GAIN MUTATED`
TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5892 TCGA-A4-A57E TCGA-B9-4117 TCGA-BQ-5889 
       49.25        11.87        11.97         8.48         0.46        10.82 
TCGA-F9-A7Q0 TCGA-G7-A8LC TCGA-GL-7966 TCGA-P4-A5EA TCGA-P4-A5EB 
       13.08        23.08         3.68         6.61        99.12 

$`11P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 
       21.86        19.23        26.04        13.25        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE 
       86.37        21.60        15.91        15.62         6.74         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
       19.63        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
       20.61         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        30.28        25.35         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       24.89        10.68         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       20.52        25.84        25.25        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
      194.79        12.92        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED 
       31.13        15.48        99.78        87.09        42.94        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.46               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             99.12             194.79 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             11.87              25.74 
[1] "0.5 - 99.1 (11.9)"  "0.1 - 194.8 (25.7)"
[1] "hr=" "4"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         4        0         5        2
  11P GAIN WILD-TYPE     167       21        47       13
D20V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  4                167
  STAGE II                 0                 21
  STAGE III                5                 47
  STAGE IV                 2                 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
  11P GAIN MUTATED     4   2     6
  11P GAIN WILD-TYPE 187  31    56
D20V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                   4                187
  T2                   2                 31
  T3+T4                6                 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"
                    vv
clus                 N0 N1 N2
  11P GAIN MUTATED    2  4  0
  11P GAIN WILD-TYPE 47 20  4
D20V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                2                 47
  N1                4                 20
  N2                0                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  2
  11P GAIN WILD-TYPE 92  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    2
  11P GAIN WILD-TYPE   92    7
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                2                 92
  1                2                  7
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5   7
  11P GAIN WILD-TYPE  71 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    7
  11P GAIN WILD-TYPE   71  205
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                5                 71
  MALE                  7                205
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 52 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3472         TCGA-AL-7173 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4114         TCGA-B9-A69E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6793 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-G7-A8LB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Y8-A8RY 
"11P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     1
  11P GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           2     9
  11P GAIN WILD-TYPE                        59   195
D20V11, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       2                 59
  WHITE                                           9                195
[1] 4 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
  11P GAIN MUTATED     0  12
  11P GAIN WILD-TYPE  12 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   12
  11P GAIN WILD-TYPE   12  228
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               12                228
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     7   3
  11Q GAIN WILD-TYPE 234  41
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                275 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 41 
$`11Q GAIN MUTATED`
TCGA-AL-A5DJ TCGA-BQ-5892 TCGA-A4-A57E TCGA-B9-4117 TCGA-F9-A7Q0 TCGA-G7-A8LC 
       49.25        11.97         8.48         0.46        13.08        23.08 
TCGA-GL-7966 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-Q2-A5QZ 
        3.68         6.61        99.12        14.07 

$`11Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       21.86        11.87        19.23        26.04        13.25        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       26.40        20.61         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        24.89        10.68         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94        92.58        52.27        16.01        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.46               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             99.12             194.79 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            12.525             25.640 
[1] "0.5 - 99.1 (12.5)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "3"  
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         4        0         4        1
  11Q GAIN WILD-TYPE     167       21        48       14
D21V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  4                167
  STAGE II                 0                 21
  STAGE III                4                 48
  STAGE IV                 1                 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
  11Q GAIN MUTATED     4   2     4
  11Q GAIN WILD-TYPE 187  31    58
D21V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   4                187
  T2                   2                 31
  T3+T4                4                 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"
                    vv
clus                 N0 N1 N2
  11Q GAIN MUTATED    2  2  0
  11Q GAIN WILD-TYPE 47 22  4
D21V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                2                 47
  N1                2                 22
  N2                0                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  1
  11Q GAIN WILD-TYPE 92  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    1
  11Q GAIN WILD-TYPE   92    8
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                2                 92
  1                1                  8
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     6   4
  11Q GAIN WILD-TYPE  70 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    4
  11Q GAIN WILD-TYPE   70  208
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                6                 70
  MALE                  4                208
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     1
  11Q GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           2     7
  11Q GAIN WILD-TYPE                        59   197
D21V11, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       2                 59
  WHITE                                           7                197
[1] 4 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
  11Q GAIN MUTATED     0  10
  11Q GAIN WILD-TYPE  12 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   10
  11Q GAIN WILD-TYPE   12  230
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               10                230
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    94  15
  12P GAIN WILD-TYPE 147  29
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               109                176 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                 29 
$`12P GAIN MUTATED`
TCGA-2Z-A9JL TCGA-2Z-A9JT TCGA-A4-7584 TCGA-AL-3468 TCGA-B3-A6W5 TCGA-B9-A5W7 
       33.07        22.49        21.37        76.64        10.16        19.23 
TCGA-BQ-5892 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6134 
       11.97        13.61        37.55         3.75        14.63        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO 
       17.95        84.89        67.17        19.73        17.75        62.83 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JG 
        7.04        75.55        59.01       100.27        56.91        54.64 
TCGA-2Z-A9JM TCGA-5P-A9K0 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-A4-7286 
       30.71        22.26        19.36        12.99        12.39        18.21 
TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 
       19.13        30.48        29.46        25.64         0.76        19.63 
TCGA-A4-8518 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 
       19.73        16.96        16.31        15.75        12.46        49.32 
TCGA-AL-7173 TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4114 
       67.73        36.49        20.32        33.83        50.50        28.18 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5877 
        1.15        43.99        22.06         0.16        17.49         8.88 
TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-7059 TCGA-BQ-7061 
       43.20        25.35        10.82         0.95         7.63         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-F9-A7Q0 TCGA-F9-A8NY 
        3.81        40.77        80.88        51.19        13.08         1.18 
TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
        4.01        39.25        25.25        17.98        23.08        16.90 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
      194.79         3.68         1.05        12.43        12.89        11.21 
TCGA-HE-7130 TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y 
       58.19        11.84        56.75        25.22        16.80         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       85.78        88.24        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EB TCGA-P4-AAVK 
       27.78        30.38        20.25        17.62        99.12        52.27 
TCGA-P4-AAVL TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SR 
       16.01        44.61        28.80        11.93        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       53.10       103.63        98.96        65.13        51.35        31.73 
TCGA-Y8-A8RY 
       25.28 

$`12P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-5P-A9JU 
       75.42        34.85        39.88        25.58        16.18        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M 
       67.17        61.05         0.89        12.99        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 
       27.68        21.07        21.86        11.87        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 TCGA-IZ-A6M8 
      129.86        35.93        24.46        13.78         3.02        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       12.13        29.26        41.33        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       15.62         6.74        58.22         4.57        91.73        56.81 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       51.52        38.99        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KE 
       78.64        15.48        71.80        62.93        43.04        27.09 
TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 
       67.43        19.63         0.10        35.18         7.82         0.23 
TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A48D 
       16.64        23.97        23.28        23.31        14.33        12.46 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.48         8.28         9.63        70.19        66.71        62.66 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3926 
        2.20        41.13        37.51        20.25        16.77        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       30.58        34.49        12.46        26.40        20.61         0.46 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
       17.23        14.86        12.30        86.76        19.27        63.72 
TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-DZ-6131 TCGA-DZ-6135 
       61.28        50.40        49.84         7.04        79.86        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G 
       34.19        19.00        24.89        10.68         2.40         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        90.90        11.05        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-7129 
       25.84        80.65        12.92        27.65        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
       26.01        73.25        19.99        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A561 TCGA-MH-A856 
       12.36        12.76        10.55        10.09        27.65        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94         6.61        92.58 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL 
       50.60        78.90        14.07        47.90        49.45        27.06 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       19.00        16.31        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        86.27        71.24        30.67        47.47 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
      110.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.16               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            194.79             129.86 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            22.490             26.025 
[1] "0.2 - 194.8 (22.5)" "0.1 - 129.9 (26.0)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED        69        8        15        8
  12P GAIN WILD-TYPE     102       13        37        7
D22V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                 69                102
  STAGE II                 8                 13
  STAGE III               15                 37
  STAGE IV                 8                  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
  12P GAIN MUTATED    75  11    24
  12P GAIN WILD-TYPE 116  22    38
D22V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                  75                116
  T2                  11                 22
  T3+T4               24                 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                 N0 N1 N2
  12P GAIN MUTATED   16 11  3
  12P GAIN WILD-TYPE 33 13  1
D22V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               16                 33
  N1               11                 13
  N2                3                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   30  4
  12P GAIN WILD-TYPE 64  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     30    4
  12P GAIN WILD-TYPE   64    5
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               30                 64
  1                4                  5
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    21  91
  12P GAIN WILD-TYPE  55 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     21   91
  12P GAIN WILD-TYPE   55  121
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               21                 55
  MALE                 91                121
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
D22V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     2
  12P GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          24    79
  12P GAIN WILD-TYPE                        37   125
D22V11, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                      24                 37
  WHITE                                          79                125
[1] 4 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
  12P GAIN MUTATED     3  97
  12P GAIN WILD-TYPE   9 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   97
  12P GAIN WILD-TYPE    9  143
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               97                143
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    94  15
  12Q GAIN WILD-TYPE 147  29
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               109                176 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                 29 
$`12Q GAIN MUTATED`
TCGA-2Z-A9JL TCGA-2Z-A9JT TCGA-A4-7584 TCGA-AL-3468 TCGA-B3-A6W5 TCGA-B9-A5W7 
       33.07        22.49        21.37        76.64        10.16        19.23 
TCGA-BQ-5892 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6134 
       11.97        13.61        37.55         3.75        14.63        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO 
       17.95        84.89        67.17        19.73        17.75        62.83 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JG 
        7.04        75.55        59.01       100.27        56.91        54.64 
TCGA-2Z-A9JM TCGA-5P-A9K0 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-A4-7286 
       30.71        22.26        19.36        12.99        12.39        18.21 
TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 
       19.13        30.48        29.46        25.64         0.76        19.63 
TCGA-A4-8518 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 
       19.73        16.96        16.31        15.75        12.46        49.32 
TCGA-AL-7173 TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4114 
       67.73        36.49        20.32        33.83        50.50        28.18 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5877 
        1.15        43.99        22.06         0.16        17.49         8.88 
TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-7059 TCGA-BQ-7061 
       43.20        25.35        10.82         0.95         7.63         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-F9-A7Q0 TCGA-F9-A8NY 
        3.81        40.77        80.88        51.19        13.08         1.18 
TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
        4.01        39.25        25.25        17.98        23.08        16.90 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
      194.79         3.68         1.05        12.43        12.89        11.21 
TCGA-HE-7130 TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y 
       58.19        11.84        56.75        25.22        16.80         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       85.78        88.24        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EB TCGA-P4-AAVK 
       27.78        30.38        20.25        17.62        99.12        52.27 
TCGA-P4-AAVL TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SR 
       16.01        44.61        28.80        11.93        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       53.10       103.63        98.96        65.13        51.35        31.73 
TCGA-Y8-A8RY 
       25.28 

$`12Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-5P-A9JU 
       75.42        34.85        39.88        25.58        16.18        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M 
       67.17        61.05         0.89        12.99        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 
       27.68        21.07        21.86        11.87        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 TCGA-IZ-A6M8 
      129.86        35.93        24.46        13.78         3.02        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       12.13        29.26        41.33        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       15.62         6.74        58.22         4.57        91.73        56.81 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       51.52        38.99        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KE 
       78.64        15.48        71.80        62.93        43.04        27.09 
TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 
       67.43        19.63         0.10        35.18         7.82         0.23 
TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A48D 
       16.64        23.97        23.28        23.31        14.33        12.46 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.48         8.28         9.63        70.19        66.71        62.66 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3926 
        2.20        41.13        37.51        20.25        16.77        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       30.58        34.49        12.46        26.40        20.61         0.46 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
       17.23        14.86        12.30        86.76        19.27        63.72 
TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-DZ-6131 TCGA-DZ-6135 
       61.28        50.40        49.84         7.04        79.86        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G 
       34.19        19.00        24.89        10.68         2.40         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        90.90        11.05        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-7129 
       25.84        80.65        12.92        27.65        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
       26.01        73.25        19.99        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A561 TCGA-MH-A856 
       12.36        12.76        10.55        10.09        27.65        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94         6.61        92.58 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL 
       50.60        78.90        14.07        47.90        49.45        27.06 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       19.00        16.31        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        86.27        71.24        30.67        47.47 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
      110.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.16               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            194.79             129.86 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            22.490             26.025 
[1] "0.2 - 194.8 (22.5)" "0.1 - 129.9 (26.0)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED        69        8        15        8
  12Q GAIN WILD-TYPE     102       13        37        7
D23V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                 69                102
  STAGE II                 8                 13
  STAGE III               15                 37
  STAGE IV                 8                  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
  12Q GAIN MUTATED    75  11    24
  12Q GAIN WILD-TYPE 116  22    38
D23V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                  75                116
  T2                  11                 22
  T3+T4               24                 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                 N0 N1 N2
  12Q GAIN MUTATED   16 11  3
  12Q GAIN WILD-TYPE 33 13  1
D23V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               16                 33
  N1               11                 13
  N2                3                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   30  4
  12Q GAIN WILD-TYPE 64  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     30    4
  12Q GAIN WILD-TYPE   64    5
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               30                 64
  1                4                  5
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    21  91
  12Q GAIN WILD-TYPE  55 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     21   91
  12Q GAIN WILD-TYPE   55  121
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               21                 55
  MALE                 91                121
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     2
  12Q GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          24    79
  12Q GAIN WILD-TYPE                        37   125
D23V11, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                      24                 37
  WHITE                                          79                125
[1] 4 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
  12Q GAIN MUTATED     3  97
  12Q GAIN WILD-TYPE   9 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   97
  12Q GAIN WILD-TYPE    9  143
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               97                143
[1] 2 2
[1] FALSE

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    25   3
  13Q GAIN WILD-TYPE 216  41
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                28                257 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 41 
$`13Q GAIN MUTATED`
TCGA-A4-A5Y1 TCGA-BQ-7046 TCGA-DW-5561 TCGA-2Z-A9J1 TCGA-4A-A93X TCGA-5P-A9K4 
       12.99        96.92        13.61        75.55        12.82        71.80 
TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-8630 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B3-8121 
       23.97        19.73        14.33         2.20        41.13        12.46 
TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-5885 TCGA-DZ-6133 TCGA-EV-5903 TCGA-G7-6790 
        0.46         1.15        30.28        51.19        24.89        51.78 
TCGA-G7-6796 TCGA-HE-7130 TCGA-MH-A856 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-SX-A7SN 
       71.44        58.19        31.13         6.61        99.12        19.00 
TCGA-SX-A7SQ TCGA-UZ-A9PX TCGA-V9-A7HT TCGA-Y8-A897 
       41.62        65.13        31.73        18.05 

$`13Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 
       44.84        26.27        20.12        11.28        48.85       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE 
       86.37        21.60        15.91        15.62         6.74         7.04 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 
        0.23        16.64        30.48        29.46        25.64        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       23.31         0.76        19.63        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B1-A47N 
       49.32        66.71        62.66        67.73        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 
       34.49        50.50        28.18        26.40        20.61        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 
       47.80        21.63        40.83        26.04        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
        7.17         3.81        40.77        79.86        80.88        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 
        0.43         4.01        90.90        11.05        39.25        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED 
       17.62        15.48        99.78        87.09        42.94        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SP 
       49.45        44.61        28.80        27.06        11.93        16.31 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        47.47       110.73        51.35        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        25.28         6.02        13.28 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.46               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             99.12             194.79 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            27.585             25.280 
[1] "0.5 - 99.1 (27.6)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "1.6"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED        18        1         5        1
  13Q GAIN WILD-TYPE     153       20        47       14
D24V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                 18                153
  STAGE II                 1                 20
  STAGE III                5                 47
  STAGE IV                 1                 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
  13Q GAIN MUTATED    21   2     5
  13Q GAIN WILD-TYPE 170  31    57
D24V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                  21                170
  T2                   2                 31
  T3+T4                5                 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"
                    vv
clus                 N0 N1 N2
  13Q GAIN MUTATED    5  3  0
  13Q GAIN WILD-TYPE 44 21  4
D24V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                5                 44
  N1                3                 21
  N2                0                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   10  0
  13Q GAIN WILD-TYPE 84  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     10    0
  13Q GAIN WILD-TYPE   84    9
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               10                 84
  1                0                  9
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     7  21
  13Q GAIN WILD-TYPE  69 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7   21
  13Q GAIN WILD-TYPE   69  191
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                7                 69
  MALE                 21                191
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           5    22
  13Q GAIN WILD-TYPE                        56   182
D24V11, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       5                 56
  WHITE                                          22                182
[1] 4 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
  13Q GAIN MUTATED     2  23
  13Q GAIN WILD-TYPE  10 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   23
  13Q GAIN WILD-TYPE   10  217
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               23                217
[1] 2 2
[1] FALSE

Clustering(25) Variable = 14Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE 239  43
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                282 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 43 
$`14Q GAIN MUTATED`
TCGA-BQ-5880 TCGA-GL-7966 TCGA-HE-7130 
       43.20         3.68        58.19 

$`14Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.68               0.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             58.19             194.79 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            43.200             25.265 
[1] "3.7 - 58.2 (43.2)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "2.3"
D25V2, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                281 
        TCGA-2Z-A9J9         TCGA-2Z-A9JD         TCGA-2Z-A9JJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JL         TCGA-2Z-A9JQ         TCGA-2Z-A9JS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JT         TCGA-5P-A9JU         TCGA-5P-A9JV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7288         TCGA-A4-7584         TCGA-A4-7734 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5Y1         TCGA-AL-3468         TCGA-AL-A5DJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A47M         TCGA-B1-A47O         TCGA-B1-A657 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B3-A6W5         TCGA-B9-5155         TCGA-B9-A44B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A5W7         TCGA-BQ-5886         TCGA-BQ-5888 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-7046         TCGA-BQ-7049 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6134         TCGA-GL-A59T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HE-A5NF         TCGA-IA-A83W         TCGA-IZ-A6M8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A855         TCGA-MH-A857         TCGA-PJ-A5Z8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-SX-A7SO         TCGA-UZ-A9PO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PZ         TCGA-Y8-A895 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A898         TCGA-Y8-A8RZ         TCGA-2K-A9WE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J1         TCGA-2Z-A9J2         TCGA-2Z-A9J3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J5         TCGA-2Z-A9J6         TCGA-2Z-A9J7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JE         TCGA-2Z-A9JG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JK         TCGA-2Z-A9JM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JN         TCGA-2Z-A9JO         TCGA-2Z-A9JP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JR         TCGA-4A-A93W         TCGA-4A-A93X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-5P-A9JW         TCGA-5P-A9JY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-5P-A9JZ         TCGA-5P-A9K0         TCGA-5P-A9K2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-5P-A9K3         TCGA-5P-A9K4         TCGA-5P-A9K6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-5P-A9K8         TCGA-5P-A9K9         TCGA-5P-A9KA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-5P-A9KC         TCGA-5P-A9KE         TCGA-5P-A9KH 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7583 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7732         TCGA-A4-7828 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8312         TCGA-A4-8515         TCGA-A4-8516 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A5Y0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A6HP         TCGA-A4-A772         TCGA-A4-A7UZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3471 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AT-A5NU         TCGA-B1-5398         TCGA-B1-7332 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A47N         TCGA-B1-A654         TCGA-B1-A655 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A656         TCGA-B3-3925         TCGA-B3-3926 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-B9-A5W8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-B9-A69E         TCGA-B9-A8YH 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A8YI         TCGA-BQ-5875         TCGA-BQ-5876 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5887 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7059 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-DZ-6131         TCGA-DZ-6132 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6135         TCGA-EV-5901 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-F9-A4JJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A7Q0         TCGA-F9-A7VF         TCGA-F9-A8NY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6789         TCGA-G7-6790 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-G7-A4TM         TCGA-G7-A8LB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A8LC         TCGA-G7-A8LD         TCGA-G7-A8LE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7773         TCGA-GL-8500 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A4EM         TCGA-GL-A59R         TCGA-GL-A9DC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-GL-A9DE         TCGA-HE-A5NH 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HE-A5NL         TCGA-IA-A40U         TCGA-IA-A40X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83S         TCGA-IA-A83T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A83V         TCGA-IZ-8195         TCGA-IZ-8196 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M9         TCGA-J7-6720         TCGA-J7-8537 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-J7-A8I2         TCGA-KV-A6GD         TCGA-KV-A6GE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KV-A74V         TCGA-MH-A55W         TCGA-MH-A55Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A560         TCGA-MH-A561         TCGA-MH-A562 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-O9-A75Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-A5E7         TCGA-P4-A5E8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-P4-A5EB         TCGA-P4-A5ED 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-P4-AAVL         TCGA-P4-AAVM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-AAVO         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU         TCGA-UN-AAZ9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PJ         TCGA-UZ-A9PK         TCGA-UZ-A9PL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PN         TCGA-UZ-A9PP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PQ         TCGA-UZ-A9PS         TCGA-UZ-A9PU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PV         TCGA-UZ-A9PX         TCGA-UZ-A9Q0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9Q1         TCGA-V9-A7HT         TCGA-Y8-A894 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A897         TCGA-Y8-A8RY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8S0         TCGA-Y8-A8S1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         0        0         3        0
  14Q GAIN WILD-TYPE     171       21        49       15
D25V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  0                171
  STAGE II                 0                 21
  STAGE III                3                 49
  STAGE IV                 0                 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
  14Q GAIN MUTATED     0   0     3
  14Q GAIN WILD-TYPE 191  33    59
D25V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                   0                191
  T2                   0                 33
  T3+T4                3                 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                 N0 N1 N2
  14Q GAIN MUTATED    0  2  0
  14Q GAIN WILD-TYPE 49 22  4
D25V5, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 75 
        TCGA-5P-A9JU         TCGA-A4-A5Y1         TCGA-B1-A47O 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A657         TCGA-BQ-5888         TCGA-BQ-5892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-IA-A83W         TCGA-Y8-A8RZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J1         TCGA-2Z-A9JO         TCGA-4A-A93W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-4A-A93X         TCGA-4A-A93Y         TCGA-5P-A9K9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A7UZ         TCGA-AL-3466 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-A655         TCGA-B1-A656 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5882         TCGA-BQ-5885 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5889         TCGA-BQ-5890 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5893         TCGA-BQ-5894 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-DW-7963         TCGA-DZ-6131 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-6846         TCGA-GL-A59R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A9DC         TCGA-IA-A40U         TCGA-IA-A40Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-J7-A8I2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KV-A74V         TCGA-P4-A5E6         TCGA-P4-A5E8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-P4-AAVK         TCGA-P4-AAVL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A7SM         TCGA-SX-A7SP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UN-AAZ9         TCGA-UZ-A9PM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PQ         TCGA-UZ-A9PX         TCGA-Y8-A897 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D25V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    2  0
  14Q GAIN WILD-TYPE 92  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    0
  14Q GAIN WILD-TYPE   92    9
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                2                 92
  1                0                  9
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE  74 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    1
  14Q GAIN WILD-TYPE   74  211
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                 74
  MALE                  1                211
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           0     2
  14Q GAIN WILD-TYPE                        61   202
D25V11, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                271 
        TCGA-2Z-A9J9         TCGA-2Z-A9JD         TCGA-2Z-A9JJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JL         TCGA-2Z-A9JQ         TCGA-2Z-A9JS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JT         TCGA-5P-A9JU         TCGA-5P-A9JV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7288         TCGA-A4-7584         TCGA-A4-7734 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5Y1         TCGA-AL-3468         TCGA-AL-A5DJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A47M         TCGA-B1-A47O         TCGA-B1-A657 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B3-A6W5         TCGA-B9-5155         TCGA-B9-A44B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A5W7         TCGA-BQ-5886         TCGA-BQ-5888 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-7046         TCGA-BQ-7049 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6134         TCGA-GL-A59T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A83W         TCGA-IZ-A6M8         TCGA-MH-A855 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A857         TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PZ         TCGA-Y8-A895         TCGA-Y8-A898 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-2K-A9WE         TCGA-2Z-A9J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J2         TCGA-2Z-A9J3         TCGA-2Z-A9J5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J6         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JG         TCGA-2Z-A9JI 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         TCGA-2Z-A9JN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-2Z-A9JP         TCGA-2Z-A9JR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-5P-A9JW         TCGA-5P-A9JY         TCGA-5P-A9JZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-5P-A9K0         TCGA-5P-A9K2         TCGA-5P-A9K3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-5P-A9K4         TCGA-5P-A9K6         TCGA-5P-A9K8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-5P-A9K9         TCGA-5P-A9KA         TCGA-5P-A9KC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-5P-A9KE         TCGA-5P-A9KH         TCGA-A4-7286 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7287         TCGA-A4-7583         TCGA-A4-7585 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7828         TCGA-A4-7915 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7996         TCGA-A4-7997         TCGA-A4-8098 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-8630         TCGA-A4-A48D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A4ZT         TCGA-A4-A57E         TCGA-A4-A5DU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5XZ         TCGA-A4-A5Y0         TCGA-A4-A6HP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A772         TCGA-A4-A7UZ         TCGA-AL-3466 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3471         TCGA-AL-3472 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-AT-A5NU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B1-A47N 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B1-A655         TCGA-B1-A656 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B3-4104         TCGA-B3-8121         TCGA-B9-4113 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5156 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A5W8         TCGA-B9-A5W9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-B9-A8YH         TCGA-B9-A8YI 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5881 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5889         TCGA-BQ-5890 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5893         TCGA-BQ-7044 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7059 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-DZ-6131         TCGA-DZ-6133 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A4JJ         TCGA-F9-A7Q0         TCGA-F9-A7VF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-6846         TCGA-GL-7773 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A9DC         TCGA-GL-A9DD         TCGA-GL-A9DE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IA-A83T         TCGA-IA-A83V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196         TCGA-IZ-A6M9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-J7-A8I2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KV-A6GD         TCGA-KV-A6GE         TCGA-KV-A74V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A55W         TCGA-MH-A55Z         TCGA-MH-A560 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A561         TCGA-MH-A562         TCGA-MH-A854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-O9-A75Z         TCGA-P4-A5E6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5E8         TCGA-P4-A5EA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-P4-A5ED         TCGA-P4-AAVK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-AAVL         TCGA-P4-AAVM         TCGA-P4-AAVO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UN-AAZ9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PJ         TCGA-UZ-A9PK         TCGA-UZ-A9PL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PN         TCGA-UZ-A9PP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PQ         TCGA-UZ-A9PS         TCGA-UZ-A9PU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PV         TCGA-UZ-A9PX         TCGA-UZ-A9Q0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9Q1         TCGA-V9-A7HT         TCGA-WN-A9G9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A897         TCGA-Y8-A8RY         TCGA-Y8-A8S0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8S1 
"14Q GAIN WILD-TYPE" 
D25V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   1
  14Q GAIN WILD-TYPE  12 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    1
  14Q GAIN WILD-TYPE   12  239
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                1                239
[1] 2 2
[1] FALSE

Clustering(26) Variable = 15Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     4   1
  15Q GAIN WILD-TYPE 237  43
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                280 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 43 
$`15Q GAIN MUTATED`
TCGA-AL-A5DJ TCGA-BQ-5892 TCGA-B1-7332 TCGA-P4-A5EB TCGA-Q2-A5QZ 
       49.25        11.97        37.51        99.12        14.07 

$`15Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       21.86        11.87        19.23        26.04        13.25        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             11.97               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             99.12             194.79 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            37.510             25.265 
[1] "12.0 - 99.1 (37.5)" "0.1 - 194.8 (25.3)"
[1] "hr=" "1"  
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         2        1         2        0
  15Q GAIN WILD-TYPE     169       20        50       15
D26V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  2                169
  STAGE II                 1                 20
  STAGE III                2                 50
  STAGE IV                 0                 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     2   1     2
  15Q GAIN WILD-TYPE 189  32    60
D26V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                   2                189
  T2                   1                 32
  T3+T4                2                 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                 N0 N1 N2
  15Q GAIN MUTATED    1  0  0
  15Q GAIN WILD-TYPE 48 24  4
D26V5, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 76 
        TCGA-5P-A9JU         TCGA-A4-A5Y1         TCGA-B1-A47O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B1-A657         TCGA-BQ-5888         TCGA-BQ-7056 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IA-A83W         TCGA-Y8-A8RZ         TCGA-2Z-A9J1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-5P-A9K9         TCGA-A4-7583 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7915         TCGA-A4-A57E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-A7UZ         TCGA-AL-3466         TCGA-AL-3472 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B9-7268 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5882         TCGA-BQ-5885 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5889         TCGA-BQ-5890 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5893         TCGA-BQ-5894 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-DW-7963         TCGA-DZ-6131 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-6846         TCGA-GL-7966 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A9DC         TCGA-IA-A40U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-6720         TCGA-J7-8537 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-J7-A8I2         TCGA-KV-A74V         TCGA-P4-A5E6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-P4-AAVK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-P4-AAVL         TCGA-SX-A71R         TCGA-SX-A7SM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SS         TCGA-UN-AAZ9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PQ         TCGA-UZ-A9PX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A897 
"15Q GAIN WILD-TYPE" 
D26V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    1  0
  15Q GAIN WILD-TYPE 93  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    0
  15Q GAIN WILD-TYPE   93    9
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                1                 93
  1                0                  9
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3   2
  15Q GAIN WILD-TYPE  73 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    2
  15Q GAIN WILD-TYPE   73  210
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 73
  MALE                  2                210
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 75 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8098 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-7963         TCGA-EV-5901 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-F9-A7Q0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-IA-A40U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-SX-A71R         TCGA-SX-A71S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SU         TCGA-UZ-A9PL         TCGA-V9-A7HT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D26V9, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 72 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         TCGA-2Z-A9JN 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-5P-A9K3         TCGA-5P-A9KE         TCGA-A4-8310 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4114         TCGA-B9-4115 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-7268         TCGA-B9-A69E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6792 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IA-A83V         TCGA-MH-A854 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E7         TCGA-SX-A71S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D26V10, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 53 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6793         TCGA-G7-6795 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-IA-A40U         TCGA-MH-A854 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E6         TCGA-P4-AAVK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     0
  15Q GAIN WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           2     3
  15Q GAIN WILD-TYPE                        59   201
D26V11, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       2                 59
  WHITE                                           3                201
[1] 4 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
  15Q GAIN MUTATED     0   5
  15Q GAIN WILD-TYPE  12 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    5
  15Q GAIN WILD-TYPE   12  235
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                5                235
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   129  21
  16P GAIN WILD-TYPE 112  23
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               150                135 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                 23 
$`16P GAIN MUTATED`
TCGA-2Z-A9JJ TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 
       39.88        25.58        16.18        22.49        61.05        21.37 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       12.99        76.64        21.67        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-7046 TCGA-BQ-7058 TCGA-DW-7834 
       11.87        19.23        26.04        96.92        11.28       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 
       35.93        24.46        61.02        17.95        84.89        16.34 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-2K-A9WE 
       17.75        62.83        21.60        15.91        15.62         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JP TCGA-2Z-A9JR 
       75.55        58.22       100.27        56.91        29.36         5.29 
TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 
       12.82       106.55        49.58        22.26        78.64        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 
       62.93        19.36        27.09        18.21         0.10        35.18 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
       16.64        30.48        25.64        23.97        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3466 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-5398 
       16.31        15.75         9.63        49.32         2.20        41.13 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       30.58        12.46        28.18         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 
       22.06         0.16        12.30        86.76        43.20        47.80 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7051 
       25.35         7.66         0.95       123.62        48.26        50.40 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-EV-5902 TCGA-EV-5903 
        7.04         3.81        40.77        51.19        19.00        24.89 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       25.15        17.98        23.08       194.79         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-A5NI TCGA-HE-A5NJ 
        1.05        12.89        11.21        81.93        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83V TCGA-IZ-8195 
       25.22        16.80         2.04        85.78        96.69        22.26 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A560 
       12.36        18.41        29.10        11.41        34.29        30.38 
TCGA-MH-A854 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       17.62        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V 
       52.27        50.60        78.90        47.90        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        53.10 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      117.40       125.29        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A897 TCGA-Y8-A8S0 
       65.13       110.73        51.35        31.73        18.05         6.02 

$`16P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7734 
       75.42        34.85        33.07        12.26        67.17         0.89 
TCGA-AL-A5DJ TCGA-B1-A47O TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 
       49.25        27.68        13.25        11.97        44.84        26.27 
TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       20.12        48.85        13.61        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-IA-A83W TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       14.63         3.02        67.17        12.13        29.26        19.73 
TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-Y8-A8RZ TCGA-2Z-A9J2 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       41.33        86.37         6.74        59.01         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 
       31.20         0.13        11.57        90.21        15.48        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7828 
       12.99        12.39        67.43        19.63        19.13         7.82 
TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
        0.23        29.46        23.28         8.28        12.46        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       66.71        62.66        67.73        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 
       16.77        20.32        33.83        29.03        34.49        50.50 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5876 
       26.40        20.61        17.23        14.86        17.49        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
        8.88        63.72        22.92        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7050 
       30.28        10.82         7.92         2.76        93.34        61.28 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
       49.84         7.63         7.17        79.86        80.88        74.60 
TCGA-EV-5901 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
       34.19        10.68        90.90        11.05        39.25        71.44 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 
       20.52        25.84        25.25        16.90        80.65        12.92 
TCGA-GL-A59R TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X 
       12.43        16.31        58.19        26.01        73.25        19.99 
TCGA-IA-A83T TCGA-IZ-8196 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55Z 
       88.24        21.34        12.76        10.55        10.09        27.78 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5ED TCGA-P4-AAVL 
       27.65        20.25        31.13        15.48        92.58        16.01 
TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       14.07        49.45        11.93        43.76        18.02        26.20 
TCGA-UZ-A9PL TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      103.63        37.35        86.27        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8S1 
       18.64        25.28        13.28 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.10               0.13 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            194.79             103.63 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             25.02              26.01 
[1] "0.1 - 194.8 (25.0)" "0.1 - 103.6 (26.0)"
[1] "hr=" "1.3"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED        90       13        27        7
  16P GAIN WILD-TYPE      81        8        25        8
D27V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                 90                 81
  STAGE II                13                  8
  STAGE III               27                 25
  STAGE IV                 7                  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
  16P GAIN MUTATED   103  19    30
  16P GAIN WILD-TYPE  88  14    32
D27V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                 103                 88
  T2                  19                 14
  T3+T4               30                 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                 N0 N1 N2
  16P GAIN MUTATED   23 13  2
  16P GAIN WILD-TYPE 26 11  2
D27V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               23                 26
  N1               13                 11
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   47  3
  16P GAIN WILD-TYPE 47  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     47    3
  16P GAIN WILD-TYPE   47    6
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               47                 47
  1                3                  6
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    28 125
  16P GAIN WILD-TYPE  48  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     28  125
  16P GAIN WILD-TYPE   48   87
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               28                 48
  MALE                125                 87
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  2     3
  16P GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          21   120
  16P GAIN WILD-TYPE                        40    84
D27V11, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                      21                 40
  WHITE                                         120                 84
[1] 4 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
  16P GAIN MUTATED     4 131
  16P GAIN WILD-TYPE   8 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4  131
  16P GAIN WILD-TYPE    8  109
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO              131                109
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   128  17
  16Q GAIN WILD-TYPE 113  27
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               145                140 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                 27 
$`16Q GAIN MUTATED`
TCGA-2Z-A9JJ TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 
       39.88        25.58        16.18        22.49        61.05        21.37 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       76.64        21.67        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-7046 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 
       19.23        26.04        96.92       129.86        35.93        24.46 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO 
       61.02        17.95        84.89        16.34        17.75        62.83 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 
       21.60        15.91        15.62         7.04        75.55        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93X TCGA-5P-A9JW 
      100.27        56.91        29.36         5.29        12.82       106.55 
TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KE 
       49.58        22.26        78.64        71.80        62.93        27.09 
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
       18.21         0.10        35.18        16.64        30.48        25.64 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3471 
       12.46        16.96         8.48        16.31        15.75        49.32 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-4117 
        2.20        41.13        30.58        12.46        28.18         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 
        1.15        43.99        22.06         0.16        12.30        86.76 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 
       43.20        47.80        25.35         0.95       123.62        48.26 
TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-EV-5902 
       50.40         7.04         3.81        40.77        51.19        19.00 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       24.89        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 
       51.78        25.15        17.98        23.08       194.79         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-A5NI 
       27.65         1.05        12.89        11.21        81.93        11.84 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83V 
       25.22        16.80        19.99         2.04        85.78        96.69 
TCGA-IZ-8195 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       22.26        12.36        18.41        29.10        11.41        34.29 
TCGA-MH-A560 TCGA-MH-A854 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       30.38        17.62        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71U 
       99.12        52.27        50.60        78.90        47.90        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       28.80        27.06        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
       53.10       117.40       125.29        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A897 
       47.47        65.13       110.73        51.35        31.73        18.05 
TCGA-Y8-A8S0 
        6.02 

$`16Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7734 
       75.42        34.85        33.07        12.26        67.17         0.89 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47O TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 
       12.99        49.25        27.68        13.25        11.97        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 
       26.27        20.12        11.28        48.85        13.61        37.55 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-IA-A83W TCGA-MH-A855 
       13.78         3.75        14.63         3.02        67.17        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-Y8-A8RZ TCGA-2Z-A9J2 
       29.26        19.73        41.33        86.37         6.74        59.01 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JZ 
       30.71        24.33        31.20         0.13        11.57        90.21 
TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH 
       15.48        43.04        19.36        12.99        12.39        67.43 
TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 
       19.63        19.13         7.82         0.23        29.46        23.28 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       67.73        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 
       33.83        29.03        34.49        50.50        26.40        20.61 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.23        14.86        17.49        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 
       22.92        21.63        40.83        26.04        30.28        10.82 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 
        7.66         7.92         2.76        93.34        61.28        49.84 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 
        7.63         7.17        79.86        80.88        74.60        34.19 
TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
       10.68        90.90        11.05        39.25        71.44        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-A59R 
       25.84        25.25        16.90        80.65        12.92        12.43 
TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A83T 
       16.31        58.19        26.01        56.75        73.25        88.24 
TCGA-IZ-8196 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55Z TCGA-MH-A561 
       21.34        12.76        10.55        10.09        27.78        27.65 
TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5ED TCGA-P4-AAVL TCGA-Q2-A5QZ 
       20.25        31.13        15.48        92.58        16.01        14.07 
TCGA-SX-A71S TCGA-SX-A7SM TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL 
       49.45        11.93        43.76        18.02        26.20       103.63 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       37.35        86.27        26.01        39.06        18.64        18.64 
TCGA-Y8-A8RY TCGA-Y8-A8S1 
       25.28        13.28 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.10               0.13 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            194.79             103.63 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             25.22              25.56 
[1] "0.1 - 194.8 (25.2)" "0.1 - 103.6 (25.6)"
[1] "hr=" "1.9"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED        91       13        24        6
  16Q GAIN WILD-TYPE      80        8        28        9
D28V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                 91                 80
  STAGE II                13                  8
  STAGE III               24                 28
  STAGE IV                 6                  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
  16Q GAIN MUTATED   102  19    26
  16Q GAIN WILD-TYPE  89  14    36
D28V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                 102                 89
  T2                  19                 14
  T3+T4               26                 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"
                    vv
clus                 N0 N1 N2
  16Q GAIN MUTATED   22 11  1
  16Q GAIN WILD-TYPE 27 13  3
D28V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               22                 27
  N1               11                 13
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   44  2
  16Q GAIN WILD-TYPE 50  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     44    2
  16Q GAIN WILD-TYPE   50    7
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               44                 50
  1                2                  7
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    28 120
  16Q GAIN WILD-TYPE  48  92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     28  120
  16Q GAIN WILD-TYPE   48   92
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               28                 48
  MALE                120                 92
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  2     3
  16Q GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          22   115
  16Q GAIN WILD-TYPE                        39    89
D28V11, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                      22                 39
  WHITE                                         115                 89
[1] 4 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
  16Q GAIN MUTATED     4 127
  16Q GAIN WILD-TYPE   8 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4  127
  16Q GAIN WILD-TYPE    8  113
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO              127                113
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED   149  20
  17P GAIN WILD-TYPE  92  24
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               169                116 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                 24 
$`17P GAIN MUTATED`
TCGA-2Z-A9JD TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 
       34.85        25.58        16.18        22.49        61.05        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 
        0.89        76.64        49.25        21.67        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-5561 
       21.86        19.23        11.97        96.92        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 
       14.63         3.02        61.02        17.95        84.89        16.34 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       17.75        62.83        86.37        21.60        15.91        15.62 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
        4.57        56.81        30.71        29.36         5.29         0.13 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        71.80        62.93 
TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
       27.09        18.21        19.13        16.64        25.64        23.97 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.31         0.76        19.63        19.73        14.33        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3471 TCGA-AL-3472 
       16.31        15.75         8.28        12.46        49.32        66.71 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4103 
        2.20        37.51        36.49        20.25        33.83        30.58 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       12.46        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5887 
       43.99        22.06         0.16        17.49        47.80        25.35 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 
        0.95         7.92        48.26        50.40         7.04         3.81 
TCGA-DW-7963 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       40.77        51.19        34.19        24.89        13.08         2.40 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
        1.18         4.01        51.78        39.25        71.44        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 
        3.68         1.05        12.43        12.89        11.21        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y 
       26.01        11.84        56.75        25.22        16.80         2.04 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.55        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA 
       30.38        27.65        20.25        15.48        87.09         6.61 
TCGA-P4-A5EB TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN 
       99.12        47.90        49.45        44.61        28.80        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      117.40       103.63       125.29        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A8RY 
       47.47        65.13       110.73        31.73        39.06        25.28 
TCGA-Y8-A8S0 
        6.02 

$`17P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-A5Y1 
       75.42        39.88        33.07        12.26        67.17        12.99 
TCGA-B1-A47O TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 
       27.68        11.87        26.04        13.25        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-IA-A83W TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       20.12        11.28        67.17        12.13        29.26        19.73 
TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
       41.33         6.74        91.73        54.64        51.52        38.99 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9K3 
       24.33        31.20        12.82        11.57       106.55        15.48 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH TCGA-A4-7287 
       43.04        19.36        12.99        12.39        67.43        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7997 TCGA-A4-8098 
        0.10        35.18         7.82         0.23        30.48        29.46 
TCGA-A4-8312 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 
       23.28        12.46         8.48         9.63        70.19        62.66 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4104 
       67.73        41.13        16.77        20.32        29.03        34.49 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       20.61        17.23        14.86        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 
       26.04        30.28        10.82         7.66         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 
       93.34        61.28        49.84         7.63         7.17        79.86 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 
       80.88        74.60        19.00        10.68         0.43        90.90 
TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE 
       11.05        25.15        20.52        12.92        27.65        16.31 
TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83S TCGA-J7-A8I2 TCGA-MH-A854 
       58.19        73.25        19.99        85.78        10.09        17.62 
TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       31.13        99.78        42.94        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-SX-A7SM TCGA-UN-AAZ9 
       50.60        78.90        14.07        27.06        11.93        18.02 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 
       37.35        86.27        51.35        26.01        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8S1 
       18.05        13.28 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.13               0.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            194.79             123.62 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             25.28              25.58 
[1] "0.1 - 194.8 (25.3)" "0.1 - 123.6 (25.6)"
[1] "hr=" "1.8"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED       117       15        17        6
  17P GAIN WILD-TYPE      54        6        35        9
D29V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                117                 54
  STAGE II                15                  6
  STAGE III               17                 35
  STAGE IV                 6                  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
  17P GAIN MUTATED   127  22    22
  17P GAIN WILD-TYPE  64  11    40
D29V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                 127                 64
  T2                  22                 11
  T3+T4               22                 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                 N0 N1 N2
  17P GAIN MUTATED   22  9  1
  17P GAIN WILD-TYPE 27 15  3
D29V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               22                 27
  N1                9                 15
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   44  3
  17P GAIN WILD-TYPE 50  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     44    3
  17P GAIN WILD-TYPE   50    6
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               44                 50
  1                3                  6
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    36 136
  17P GAIN WILD-TYPE  40  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     36  136
  17P GAIN WILD-TYPE   40   76
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               36                 40
  MALE                136                 76
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  2     4
  17P GAIN WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          29   129
  17P GAIN WILD-TYPE                        32    75
D29V11, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           4                  2
  BLACK OR AFRICAN AMERICAN                      29                 32
  WHITE                                         129                 75
[1] 4 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
  17P GAIN MUTATED     4 154
  17P GAIN WILD-TYPE   8  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4  154
  17P GAIN WILD-TYPE    8   86
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO              154                 86
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   161  27
  17Q GAIN WILD-TYPE  80  17
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               188                 97 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                27                 17 
$`17Q GAIN MUTATED`
TCGA-2Z-A9JD TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 
       34.85        25.58        16.18        22.49        61.05        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
        0.89        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       11.97        96.92        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-PJ-A5Z9 
        3.02        61.02        17.95        84.89        16.34        17.75 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-2K-A9WE 
       62.83        86.37        21.60        15.91        15.62         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       56.81        51.52        30.71        29.36         5.29         0.13 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7915 
       62.93        19.36        27.09        18.21        19.13         0.23 
TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       16.64        25.64        23.97        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU 
        8.28        12.46         9.63        49.32        66.71         2.20 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-4103 
       37.51        36.49        20.25        16.77        33.83        30.58 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       12.46        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5881 
       43.99        22.06         0.16        17.49        86.76        47.80 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7051 
       25.35         7.66         0.95         7.92        48.26        50.40 
TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
       49.84         7.04         3.81        40.77        80.88        51.19 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
       34.19        24.89        13.08         2.40         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM 
       51.78        11.05        39.25        71.44        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 
       17.98        23.08        16.90        80.65       194.79         3.68 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-A5NH 
        1.05        12.43        12.89        11.21        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83T 
       11.84        56.75        25.22        16.80         2.04        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB 
       27.65        20.25        15.48        87.09         6.61        99.12 
TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       16.01        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS 
       26.20       117.40       103.63       125.29        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-AB4C 
       30.67        47.47        65.13       110.73        31.73        39.06 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

$`17Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-A5Y1 
       75.42        39.88        33.07        12.26        67.17        12.99 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-IA-A83W TCGA-MH-A855 TCGA-MH-A857 
       44.84        26.27        20.12        67.17        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JK 
       19.73        41.33         6.74        91.73        54.64        38.99 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9K8 
       24.33        31.20        12.82        11.57       106.55        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       12.99        12.39        67.43        19.63         0.10        35.18 
TCGA-A4-7828 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A48D TCGA-AL-3467 
        7.82        30.48        29.46        23.28        12.46        70.19 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4104 
       62.66        67.73        41.13        20.32        29.03        34.49 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 
       20.61        17.23        14.86        12.30        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 
       30.28        10.82         2.76       123.62        93.34        61.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ 
        7.63         7.17        79.86        74.60        19.00        10.68 
TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 
        0.43        90.90        25.15        20.52        12.92        27.65 
TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83S TCGA-J7-A8I2 
       16.31        58.19        73.25        19.99        85.78        10.09 
TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK 
       17.62        31.13        99.78        42.94        92.58        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A7SL TCGA-SX-A7SM TCGA-UN-AAZ9 TCGA-UZ-A9PN 
       50.60        78.90        27.06        11.93        18.02        37.35 
TCGA-UZ-A9PQ TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       86.27        51.35        26.01        18.64        18.64        18.05 
TCGA-Y8-A8S1 
       13.28 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.13               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            194.79             123.62 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            24.675             27.060 
[1] "0.1 - 194.8 (24.7)" "0.1 - 123.6 (27.1)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED       121       16        26        9
  17Q GAIN WILD-TYPE      50        5        26        6
D30V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                121                 50
  STAGE II                16                  5
  STAGE III               26                 26
  STAGE IV                 9                  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
  17Q GAIN MUTATED   131  25    34
  17Q GAIN WILD-TYPE  60   8    28
D30V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                 131                 60
  T2                  25                  8
  T3+T4               34                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17Q GAIN MUTATED   29 10  3
  17Q GAIN WILD-TYPE 20 14  1
D30V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               29                 20
  N1               10                 14
  N2                3                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   51  5
  17Q GAIN WILD-TYPE 43  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     51    5
  17Q GAIN WILD-TYPE   43    4
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               51                 43
  1                5                  4
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    45 146
  17Q GAIN WILD-TYPE  31  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     45  146
  17Q GAIN WILD-TYPE   31   66
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               45                 31
  MALE                146                 66
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  2     4
  17Q GAIN WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          33   143
  17Q GAIN WILD-TYPE                        28    61
D30V11, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           4                  2
  BLACK OR AFRICAN AMERICAN                      33                 28
  WHITE                                         143                 61
[1] 4 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
  17Q GAIN MUTATED     6 167
  17Q GAIN WILD-TYPE   6  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  167
  17Q GAIN WILD-TYPE    6   73
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  6
  NOT HISPANIC OR LATINO              167                 73
[1] 2 2
[1] FALSE

Clustering(31) Variable = 18P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    10   2
  18P GAIN WILD-TYPE 231  42
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                273 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 42 
$`18P GAIN MUTATED`
TCGA-A4-A5Y1 TCGA-B9-5155 TCGA-DW-5560 TCGA-2Z-A9J1 TCGA-AL-3466 TCGA-B3-4103 
       12.99        21.86        48.85        75.55         9.63        30.58 
TCGA-B3-4104 TCGA-G7-6790 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-HE-A5NJ TCGA-SX-A7SS 
       34.49        51.78        17.98        23.08        56.75        53.10 

$`18P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5561 TCGA-DW-7834 
       44.84        26.27        20.12        11.28        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE 
       86.37        21.60        15.91        15.62         6.74         7.04 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       71.80        62.93        43.04        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
       15.75         8.28        12.46        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 
       20.25        16.77        20.32        33.83        29.03        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.84        25.25        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK 
       16.31        81.93        58.19        26.01        11.84        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       16.31        41.62        26.47        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              9.63               0.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             75.55             194.79 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            32.535             25.250 
[1] "9.6 - 75.5 (32.5)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "1"  
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         6        1         2        2
  18P GAIN WILD-TYPE     165       20        50       13
D31V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  6                165
  STAGE II                 1                 20
  STAGE III                2                 50
  STAGE IV                 2                 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
  18P GAIN MUTATED     8   2     2
  18P GAIN WILD-TYPE 183  31    60
D31V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   8                183
  T2                   2                 31
  T3+T4                2                 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                 N0 N1 N2
  18P GAIN MUTATED    2  2  0
  18P GAIN WILD-TYPE 47 22  4
D31V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                2                 47
  N1                2                 22
  N2                0                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    5  1
  18P GAIN WILD-TYPE 89  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    1
  18P GAIN WILD-TYPE   89    8
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                5                 89
  1                1                  8
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1  11
  18P GAIN WILD-TYPE  75 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   11
  18P GAIN WILD-TYPE   75  201
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                 75
  MALE                 11                201
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 52 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6793         TCGA-G7-6795 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LD         TCGA-G7-A8LE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-UZ-A9PM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-Y8-A8RY 
"18P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           0    11
  18P GAIN WILD-TYPE                        61   193
D31V11, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 61
  WHITE                                          11                193
[1] 4 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
  18P GAIN MUTATED     0  11
  18P GAIN WILD-TYPE  12 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   11
  18P GAIN WILD-TYPE   12  229
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               11                229
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     9   0
  18Q GAIN WILD-TYPE 232  44
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                276 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                 44 
$`18Q GAIN MUTATED`
TCGA-B9-5155 TCGA-DW-5560 TCGA-2Z-A9J1 TCGA-B3-4103 TCGA-B3-4104 TCGA-G7-6790 
       21.86        48.85        75.55        30.58        34.49        51.78 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-SX-A7SS 
       17.98        23.08        53.10 

$`18Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       10.16        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5561 
       96.92        44.84        26.27        20.12        11.28        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       29.03        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43         4.01        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE 
       25.15        20.52        25.84        25.25        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             17.98               0.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             75.55             194.79 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            34.490             25.235 
[1] "18.0 - 75.5 (34.5)" "0.1 - 194.8 (25.2)"
[1] "hr="     "2.6e+07"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         6        1         1        1
  18Q GAIN WILD-TYPE     165       20        51       14
D32V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  6                165
  STAGE II                 1                 20
  STAGE III                1                 51
  STAGE IV                 1                 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
  18Q GAIN MUTATED     6   2     1
  18Q GAIN WILD-TYPE 185  31    61
D32V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                   6                185
  T2                   2                 31
  T3+T4                1                 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"
                    vv
clus                 N0 N1 N2
  18Q GAIN MUTATED    2  0  0
  18Q GAIN WILD-TYPE 47 24  4
D32V5, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 75 
        TCGA-5P-A9JU         TCGA-A4-A5Y1         TCGA-B1-A47O 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-A657         TCGA-BQ-5888         TCGA-BQ-5892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-IA-A83W         TCGA-Y8-A8RZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-5P-A9K9         TCGA-A4-7583 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7915         TCGA-A4-A57E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-A7UZ         TCGA-AL-3466         TCGA-AL-3472 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B9-7268 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5882         TCGA-BQ-5885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5889         TCGA-BQ-5890 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-DW-7963         TCGA-DZ-6131 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-6846         TCGA-GL-7966 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A9DC         TCGA-IA-A40U 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-6720         TCGA-J7-8537 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-J7-A8I2         TCGA-KV-A74V         TCGA-P4-A5E6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-P4-AAVK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-AAVL         TCGA-SX-A71R         TCGA-SX-A7SM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-UN-AAZ9         TCGA-UZ-A9PM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PQ         TCGA-UZ-A9PX         TCGA-Y8-A897 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D32V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  0
  18Q GAIN WILD-TYPE 90  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE   90    9
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                4                 90
  1                0                  9
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1   8
  18Q GAIN WILD-TYPE  75 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    8
  18Q GAIN WILD-TYPE   75  204
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 75
  MALE                  8                204
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 72 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         TCGA-2Z-A9JN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-5P-A9K3         TCGA-5P-A9KE         TCGA-A4-8310 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4114         TCGA-B9-4115 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-7268         TCGA-B9-A69E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6792 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A83V         TCGA-MH-A854         TCGA-MH-A856 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-Q2-A5QZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-UZ-A9PM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D32V10, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 52 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6793         TCGA-G7-6795 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LD         TCGA-G7-A8LE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-UZ-A9PM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY 
"18Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0     9
  18Q GAIN WILD-TYPE                        61   195
D32V11, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 61
  WHITE                                           9                195
[1] 4 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
  18Q GAIN MUTATED     0   9
  18Q GAIN WILD-TYPE  12 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    9
  18Q GAIN WILD-TYPE   12  231
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                9                231
[1] 2 2
[1] FALSE

Clustering(33) Variable = 19P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     5   0
  19P GAIN WILD-TYPE 236  44
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                280 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                 44 
$`19P GAIN MUTATED`
TCGA-BQ-5892 TCGA-BQ-5885 TCGA-F9-A7Q0 TCGA-G7-A8LC TCGA-GL-7966 
       11.97        30.28        13.08        23.08         3.68 

$`19P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 
       43.20        47.80        21.63        40.83        26.04        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              3.68               0.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             30.28             194.79 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            13.080             25.465 
[1] "3.7 - 30.3 (13.1)"  "0.1 - 194.8 (25.5)"
[1] "hr="     "3300000"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         3        0         2        0
  19P GAIN WILD-TYPE     168       21        50       15
D33V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  3                168
  STAGE II                 0                 21
  STAGE III                2                 50
  STAGE IV                 0                 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 GAIN MUTATED     3   0     2
  19P GAIN WILD-TYPE 188  33    60
D33V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                   3                188
  T2                   0                 33
  T3+T4                2                 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                 N0 N1 N2
  19P GAIN MUTATED    2  1  0
  19P GAIN WILD-TYPE 47 23  4
D33V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                2                 47
  N1                1                 23
  N2                0                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    3  0
  19P GAIN WILD-TYPE 91  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    0
  19P GAIN WILD-TYPE   91    9
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                3                 91
  1                0                  9
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2   3
  19P GAIN WILD-TYPE  74 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    3
  19P GAIN WILD-TYPE   74  209
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                2                 74
  MALE                  3                209
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 74 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8098 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-7963         TCGA-EV-5901 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-J7-8537         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-SX-A7SU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-UZ-A9PL         TCGA-V9-A7HT 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D33V9, continuous
D33V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     1
  19P GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           0     4
  19P GAIN WILD-TYPE                        61   200
D33V11, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       0                 61
  WHITE                                           4                200
[1] 4 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
  19P GAIN MUTATED     0   5
  19P GAIN WILD-TYPE  12 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    5
  19P GAIN WILD-TYPE   12  235
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                5                235
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED     5   0
  19Q GAIN WILD-TYPE 236  44
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                280 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                 44 
$`19Q GAIN MUTATED`
TCGA-BQ-5892 TCGA-BQ-5885 TCGA-F9-A7Q0 TCGA-G7-A8LC TCGA-GL-7966 
       11.97        30.28        13.08        23.08         3.68 

$`19Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 
       43.20        47.80        21.63        40.83        26.04        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              3.68               0.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             30.28             194.79 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            13.080             25.465 
[1] "3.7 - 30.3 (13.1)"  "0.1 - 194.8 (25.5)"
[1] "hr="     "3300000"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         3        0         2        0
  19Q GAIN WILD-TYPE     168       21        50       15
D34V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  3                168
  STAGE II                 0                 21
  STAGE III                2                 50
  STAGE IV                 0                 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
  19Q GAIN MUTATED     3   0     2
  19Q GAIN WILD-TYPE 188  33    60
D34V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                   3                188
  T2                   0                 33
  T3+T4                2                 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                 N0 N1 N2
  19Q GAIN MUTATED    2  1  0
  19Q GAIN WILD-TYPE 47 23  4
D34V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                2                 47
  N1                1                 23
  N2                0                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    3  0
  19Q GAIN WILD-TYPE 91  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3    0
  19Q GAIN WILD-TYPE   91    9
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                3                 91
  1                0                  9
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2   3
  19Q GAIN WILD-TYPE  74 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    3
  19Q GAIN WILD-TYPE   74  209
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                2                 74
  MALE                  3                209
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 74 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8098 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-7963         TCGA-EV-5901 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-J7-8537         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-SX-A7SU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PL         TCGA-V9-A7HT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D34V9, continuous
D34V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     1
  19Q GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           0     4
  19Q GAIN WILD-TYPE                        61   200
D34V11, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       0                 61
  WHITE                                           4                200
[1] 4 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
  19Q GAIN MUTATED     0   5
  19Q GAIN WILD-TYPE  12 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    5
  19Q GAIN WILD-TYPE   12  235
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                5                235
[1] 2 2
[1] FALSE

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    84  13
  20P GAIN WILD-TYPE 157  31
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                97                188 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                 31 
$`20P GAIN MUTATED`
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-BQ-5892 
       16.18        22.49         0.89        12.99        76.64        11.97 
TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 TCGA-HE-A5NF 
       96.92        48.85        13.61        35.93        14.63        84.89 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-2K-A9WE TCGA-2Z-A9J1 
       17.75        62.83        21.60        15.91         7.04        75.55 
TCGA-2Z-A9J7 TCGA-2Z-A9JG TCGA-2Z-A9JM TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JY 
        4.57        54.64        30.71         0.13        12.82        49.58 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-A4-7286 
       22.26        78.64        71.80        62.93        19.36        18.21 
TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8517 
       19.13        16.64        30.48        25.64        23.97        19.63 
TCGA-A4-8518 TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3466 TCGA-AL-3471 TCGA-AT-A5NU 
       19.73        16.31        15.75         9.63        49.32         2.20 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
       37.51        36.49        20.25        33.83        30.58        12.46 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5882 
        0.46         1.15        22.06         0.16        17.49        21.63 
TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DZ-6132 
       25.35         0.95         2.76        50.40         3.81        80.88 
TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6789 TCGA-G7-6795 
       51.19        19.00        13.08         2.40         4.01        39.25 
TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-7130 TCGA-HE-A5NI 
       25.15        17.98        23.08         3.68        58.19        11.84 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
        2.04        22.26        10.09        18.41        29.10        34.29 
TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-Q2-A5QZ TCGA-SX-A71R 
       20.25        17.62         6.61        52.27        14.07        47.90 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PL 
       28.80        27.06        16.31        41.62        53.10       103.63 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-AB4C 
       98.96        71.24        47.47       110.73        31.73        39.06 
TCGA-Y8-A8S0 
        6.02 

$`20P GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-5P-A9JU 
       75.42        34.85        39.88        33.07        25.58        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       67.17        61.05        21.37        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7834 
       13.25        44.84        26.27        20.12        11.28       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6134 
       37.55        24.46        13.78         3.75         3.02        61.02 
TCGA-GL-A59T TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       17.95        67.17        16.34        12.13        29.26        19.73 
TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       41.33        86.37        15.62         6.74        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK 
      100.27        56.91        91.73        56.81        51.52        38.99 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93Y TCGA-5P-A9JW 
       24.33        31.20        29.36         5.29        11.57       106.55 
TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       90.21        15.48        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 
       67.43        19.63         0.10        35.18         7.82         0.23 
TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D 
       29.46        23.28        23.31         0.76        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
       16.96         8.48         8.28        12.46        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 
       62.66        67.73        41.13        16.77        20.32        29.03 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 
       34.49        50.50        28.18        26.40        20.61        43.99 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23        14.86        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
       30.28        10.82         7.66         7.92       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       93.34        61.28        49.84         7.63         7.04         7.17 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
       40.77        79.86        74.60        34.19        24.89        10.68 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
        1.18         0.43        51.78        90.90        11.05        71.44 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       20.52        25.84        25.25        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       16.31        81.93        26.01        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 
       16.80        19.99        85.78        88.24        96.69        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 
       12.36        12.76        10.55        11.41        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       27.65        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71S 
       99.12        92.58        16.01        50.60        78.90        49.45 
TCGA-SX-A71U TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 
       44.61        11.93        19.00        26.47        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PU 
       26.20       117.40       125.29        37.35        86.27        30.67 
TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       65.13        51.35        26.01        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S1 
       25.28        13.28 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.13               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            110.73             194.79 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            21.630             26.235 
[1] "0.1 - 110.7 (21.6)" "0.1 - 194.8 (26.2)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED        58       10        15        6
  20P GAIN WILD-TYPE     113       11        37        9
D35V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 58                113
  STAGE II                10                 11
  STAGE III               15                 37
  STAGE IV                 6                  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
  20P GAIN MUTATED    65  15    19
  20P GAIN WILD-TYPE 126  18    43
D35V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                  65                126
  T2                  15                 18
  T3+T4               19                 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                 N0 N1 N2
  20P GAIN MUTATED   13  9  2
  20P GAIN WILD-TYPE 36 15  2
D35V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               13                 36
  N1                9                 15
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   32  3
  20P GAIN WILD-TYPE 62  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     32    3
  20P GAIN WILD-TYPE   62    6
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               32                 62
  1                3                  6
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    26  73
  20P GAIN WILD-TYPE  50 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     26   73
  20P GAIN WILD-TYPE   50  139
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               26                 50
  MALE                 73                139
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     2
  20P GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          16    73
  20P GAIN WILD-TYPE                        45   131
D35V11, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                      16                 45
  WHITE                                          73                131
[1] 4 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
  20P GAIN MUTATED     3  84
  20P GAIN WILD-TYPE   9 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   84
  20P GAIN WILD-TYPE    9  156
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               84                156
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    85  14
  20Q GAIN WILD-TYPE 156  30
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                99                186 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                14                 30 
$`20Q GAIN MUTATED`
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-BQ-5892 
       16.18        22.49         0.89        12.99        76.64        11.97 
TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 TCGA-HE-A5NF 
       96.92        48.85        13.61        35.93        14.63        84.89 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-2K-A9WE TCGA-2Z-A9J1 
       17.75        62.83        21.60        15.91         7.04        75.55 
TCGA-2Z-A9J7 TCGA-2Z-A9JG TCGA-2Z-A9JM TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JY 
        4.57        54.64        30.71         0.13        12.82        49.58 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-A4-7286 
       22.26        78.64        71.80        62.93        19.36        18.21 
TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8517 
       19.13        16.64        30.48        25.64        23.97        19.63 
TCGA-A4-8518 TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3466 TCGA-AL-3471 TCGA-AT-A5NU 
       19.73        16.31        15.75         9.63        49.32         2.20 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       37.51        36.49        20.25        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH 
       12.46         0.46         1.15        22.06         0.16        17.49 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7051 
       22.92        21.63        25.35         0.95         2.76        50.40 
TCGA-BQ-7062 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF 
        3.81        80.88        51.19        19.00        13.08         2.40 
TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7966 
        4.01        39.25        25.15        17.98        23.08         3.68 
TCGA-HE-7130 TCGA-HE-A5NI TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-A8I2 TCGA-KV-A6GD 
       58.19        11.84         2.04        22.26        10.09        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EA TCGA-P4-AAVK 
       29.10        34.29        20.25        17.62         6.61        52.27 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SP 
       78.90        14.07        47.90        28.80        27.06        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PV TCGA-UZ-A9Q0 
       41.62        53.10       103.63        98.96        47.47       110.73 
TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A8S0 
       31.73        39.06         6.02 

$`20Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-5P-A9JU 
       75.42        34.85        39.88        33.07        25.58        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       67.17        61.05        21.37        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7834 
       13.25        44.84        26.27        20.12        11.28       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6134 
       37.55        24.46        13.78         3.75         3.02        61.02 
TCGA-GL-A59T TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       17.95        67.17        16.34        12.13        29.26        19.73 
TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       41.33        86.37        15.62         6.74        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK 
      100.27        56.91        91.73        56.81        51.52        38.99 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93Y TCGA-5P-A9JW 
       24.33        31.20        29.36         5.29        11.57       106.55 
TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       90.21        15.48        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 
       67.43        19.63         0.10        35.18         7.82         0.23 
TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D 
       29.46        23.28        23.31         0.76        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
       16.96         8.48         8.28        12.46        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 
       62.66        67.73        41.13        16.77        20.32        29.03 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-A5W8 
       50.50        28.18        26.40        20.61        43.99        17.23 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 
       43.20        47.80        40.83        26.04        30.28        10.82 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.66         7.92       123.62        48.26        93.34        61.28 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7963 TCGA-DZ-6131 
       49.84         7.63         7.04         7.17        40.77        79.86 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G 
       74.60        34.19        24.89        10.68         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       51.78        90.90        11.05        71.44        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       25.25        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       26.01        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       85.78        88.24        96.69        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A856 
       10.55        11.41        27.78        30.38        27.65        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94        99.12        92.58 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SM TCGA-SX-A7SN 
       16.01        50.60        49.45        44.61        11.93        19.00 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        43.76        18.02        26.20       117.40       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q1 
       37.35        86.27        71.24        30.67        65.13        51.35 
TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S1 
       26.01        18.64        18.64        18.05        25.28        13.28 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.13               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            110.73             194.79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            22.060             26.235 
[1] "0.1 - 110.7 (22.1)" "0.1 - 194.8 (26.2)"
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED        59       10        16        6
  20Q GAIN WILD-TYPE     112       11        36        9
D36V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 59                112
  STAGE II                10                 11
  STAGE III               16                 36
  STAGE IV                 6                  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
  20Q GAIN MUTATED    66  15    20
  20Q GAIN WILD-TYPE 125  18    42
D36V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                  66                125
  T2                  15                 18
  T3+T4               20                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  20Q GAIN MUTATED   13 10  2
  20Q GAIN WILD-TYPE 36 14  2
D36V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               13                 36
  N1               10                 14
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   34  3
  20Q GAIN WILD-TYPE 60  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     34    3
  20Q GAIN WILD-TYPE   60    6
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               34                 60
  1                3                  6
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    26  75
  20Q GAIN WILD-TYPE  50 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     26   75
  20Q GAIN WILD-TYPE   50  137
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               26                 50
  MALE                 75                137
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     2
  20Q GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          15    76
  20Q GAIN WILD-TYPE                        46   128
D36V11, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                      15                 46
  WHITE                                          76                128
[1] 4 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
  20Q GAIN MUTATED     3  85
  20Q GAIN WILD-TYPE   9 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   85
  20Q GAIN WILD-TYPE    9  155
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               85                155
[1] 2 2
[1] FALSE

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    17   2
  21Q GAIN WILD-TYPE 224  42
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                266 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 42 
$`21Q GAIN MUTATED`
TCGA-2Z-A9JS TCGA-A4-7584 TCGA-B1-A47O TCGA-BQ-5892 TCGA-UZ-A9PZ TCGA-2K-A9WE 
       16.18        21.37        27.68        11.97        21.60         7.04 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-A6HP TCGA-AT-A5NU TCGA-B9-4117 TCGA-B9-A5W9 
       23.97        23.31        12.46         2.20         0.46         0.16 
TCGA-F9-A8NY TCGA-G7-A8LC TCGA-HE-A5NJ TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UZ-A9PK 
        1.18        23.08        56.75         6.61        14.07       117.40 
TCGA-UZ-A9Q0 
      110.73 

$`21Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JT 
       75.42        34.85        39.88        33.07        25.58        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       12.26        67.17        61.05         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       49.25        21.67        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       19.23        26.04        13.25        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.91        15.62         6.74        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 
        0.23        16.64        30.48        29.46        25.64        23.28 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 
        8.48        16.31        15.75         8.28         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       49.32        66.71        62.66        67.73        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E 
       20.61         1.15        43.99        22.06        17.23        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 
       24.89        10.68        13.08         2.40         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       20.52        25.84        25.25        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       11.84        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       31.13        15.48        99.78        87.09        42.94        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       26.20       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       71.24        30.67        47.47        65.13        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.16               0.10 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            117.40             194.79 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             16.18              26.01 
[1] "0.2 - 117.4 (16.2)" "0.1 - 194.8 (26.0)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED        12        1         3        1
  21Q GAIN WILD-TYPE     159       20        49       14
D37V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                 12                159
  STAGE II                 1                 20
  STAGE III                3                 49
  STAGE IV                 1                 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
  21Q GAIN MUTATED    13   2     4
  21Q GAIN WILD-TYPE 178  31    58
D37V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                  13                178
  T2                   2                 31
  T3+T4                4                 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"
                    vv
clus                 N0 N1 N2
  21Q GAIN MUTATED    2  2  0
  21Q GAIN WILD-TYPE 47 22  4
D37V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                2                 47
  N1                2                 22
  N2                0                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  1
  21Q GAIN WILD-TYPE 91  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    1
  21Q GAIN WILD-TYPE   91    8
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                3                 91
  1                1                  8
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     5  14
  21Q GAIN WILD-TYPE  71 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5   14
  21Q GAIN WILD-TYPE   71  198
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                5                 71
  MALE                 14                198
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
D37V10, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 52 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-7963         TCGA-F9-A97G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-SX-A71S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY 
"21Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1     1
  21Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           3    13
  21Q GAIN WILD-TYPE                        58   191
D37V11, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       3                 58
  WHITE                                          13                191
[1] 4 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
  21Q GAIN MUTATED     1  17
  21Q GAIN WILD-TYPE  11 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   17
  21Q GAIN WILD-TYPE   11  223
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               17                223
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     3   1
  22Q GAIN WILD-TYPE 238  43
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                281 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 43 
$`22Q GAIN MUTATED`
TCGA-BQ-5892 TCGA-5P-A9K9 TCGA-G7-A8LB TCGA-V9-A7HT 
       11.97        19.36        17.98        31.73 

$`22Q GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       65.13       110.73        51.35        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             11.97               0.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             31.73             194.79 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             18.67              25.35 
[1] "12.0 - 31.7 (18.7)" "0.1 - 194.8 (25.4)"
[1] "hr=" "3"  
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         2        1         0        1
  22Q GAIN WILD-TYPE     169       20        52       14
D38V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  2                169
  STAGE II                 1                 20
  STAGE III                0                 52
  STAGE IV                 1                 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
  22Q GAIN MUTATED     2   2     1
  22Q GAIN WILD-TYPE 189  31    61
D38V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                   2                189
  T2                   2                 31
  T3+T4                1                 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"
                    vv
clus                 N0 N1 N2
  22Q GAIN MUTATED    1  0  1
  22Q GAIN WILD-TYPE 48 24  3
D38V5, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 75 
        TCGA-5P-A9JU         TCGA-A4-A5Y1         TCGA-B1-A47O 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B1-A657         TCGA-BQ-5888         TCGA-BQ-7056 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IA-A83W         TCGA-Y8-A8RZ         TCGA-2Z-A9J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-7583         TCGA-A4-7585 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-A57E         TCGA-A4-A7UZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-3473 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-A655 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B1-A656         TCGA-B9-7268         TCGA-BQ-5877 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5885         TCGA-BQ-5887 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-DZ-6131         TCGA-F9-A8NY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6789         TCGA-G7-6793 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-G7-A8LD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-GL-A59R 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GL-A9DC         TCGA-IA-A40U         TCGA-IA-A40Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-J7-A8I2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KV-A74V         TCGA-P4-A5E6         TCGA-P4-A5E8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-P4-AAVK         TCGA-P4-AAVL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A7SM         TCGA-SX-A7SP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UN-AAZ9         TCGA-UZ-A9PM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PQ         TCGA-UZ-A9PX         TCGA-Y8-A897 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D38V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    1  0
  22Q GAIN WILD-TYPE 93  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    0
  22Q GAIN WILD-TYPE   93    9
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                1                 93
  1                0                  9
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1   4
  22Q GAIN WILD-TYPE  75 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    4
  22Q GAIN WILD-TYPE   75  208
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                1                 75
  MALE                  4                208
[1] 2 2
[1] FALSE
D38V8, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 74 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8098 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-7963         TCGA-EV-5901 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-F9-A7Q0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LC         TCGA-G7-A8LD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-P4-AAVK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SU         TCGA-UZ-A9PL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D38V9, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 73 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         TCGA-2Z-A9JN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-5P-A9K3         TCGA-5P-A9KE         TCGA-A4-8310 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4114         TCGA-B9-4115 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-7268         TCGA-B9-A69E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6792 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IA-A83V         TCGA-MH-A854         TCGA-MH-A856 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-Q2-A5QZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY 
"22Q GAIN WILD-TYPE" 
D38V10, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 53 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6793         TCGA-G7-6795 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LD         TCGA-G7-A8LE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           1     4
  22Q GAIN WILD-TYPE                        60   200
D38V11, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       1                 60
  WHITE                                           4                200
[1] 4 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
  22Q GAIN MUTATED     1   4
  22Q GAIN WILD-TYPE  11 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    4
  22Q GAIN WILD-TYPE   11  236
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                4                236
[1] 2 2
[1] FALSE

Clustering(39) Variable = XP GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    75  11
  XP GAIN WILD-TYPE 166  33
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               86               199 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               11                33 
$`XP GAIN MUTATED`
TCGA-2Z-A9JQ TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-BQ-7046 
       25.58        76.64        21.67        21.07        10.16        96.92 
TCGA-DW-5561 TCGA-DW-7836 TCGA-GL-A59T TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-UZ-A9PO 
       13.61        35.93        17.95        84.89        17.75        62.83 
TCGA-Y8-A895 TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       15.91        75.55        59.01        58.22       100.27        56.91 
TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 TCGA-A4-8311 TCGA-A4-8515 
       49.58        22.26        78.64        62.93        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
        0.76        19.63        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B3-4103 
       15.75        12.46        49.32         2.20        36.49        30.58 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A5W9 
       50.50        28.18         0.46         1.15        43.99         0.16 
TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7060 
       17.49        47.80         0.95         7.92        48.26         7.04 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
        3.81        40.77        51.19         2.40         1.18        51.78 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 TCGA-HE-7129 TCGA-HE-7130 
       39.25        25.25        17.98       194.79        81.93        58.19 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       11.84        56.75        25.22        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL 
       34.29        27.78        87.09        99.12        52.27        16.01 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       44.61        28.80        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       53.10       117.40        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       51.35        31.73 

$`XP GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        39.88        33.07        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-A5DJ TCGA-B1-A47O TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       49.25        27.68        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       13.25        11.97        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       48.85       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       14.63         3.02        61.02        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A898 
       29.26        19.73        41.33        86.37        21.60        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
        6.74         7.04         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
        5.29         0.13        12.82        11.57       106.55        90.21 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        43.04        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 
       25.64        23.28        19.73         8.48         8.28         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       70.19        66.71        62.66        67.73        41.13        37.51 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 
       20.25        16.77        20.32        33.83        29.03        34.49 
TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E 
       12.46        26.40        20.61        22.06        17.23        14.86 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 
       10.82         7.66         2.76       123.62        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 
       50.40        49.84         7.63         7.17        79.86        80.88 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
        0.43         4.01        90.90        11.05        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 
       20.52        25.84        23.08        16.90        80.65        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       16.31        26.01        73.25        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       12.76        10.55        10.09        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA 
       17.62        31.13        15.48        99.78        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL 
       27.06        11.93        43.76        18.02        26.20       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 
      125.29        37.35        98.96        86.27        71.24        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.16              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           194.79            129.86 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            28.95             23.28 
[1] "0.2 - 194.8 (29.0)" "0.1 - 129.9 (23.3)"
[1] "hr=" "1.5"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED        62        7         6        4
  XP GAIN WILD-TYPE     109       14        46       11
D39V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                62               109
  STAGE II                7                14
  STAGE III               6                46
  STAGE IV                4                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
  XP GAIN MUTATED    68  11     9
  XP GAIN WILD-TYPE 123  22    53
D39V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T1                 68               123
  T2                 11                22
  T3+T4               9                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                N0 N1 N2
  XP GAIN MUTATED   11  4  0
  XP GAIN WILD-TYPE 38 20  4
D39V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              11                38
  N1               4                20
  N2               0                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   26  2
  XP GAIN WILD-TYPE 68  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     26    2
  XP GAIN WILD-TYPE   68    7
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              26                68
  1               2                 7
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    15  73
  XP GAIN WILD-TYPE  61 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     15   73
  XP GAIN WILD-TYPE   61  139
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              15                61
  MALE                73               139
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
D39V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  2     1
  XP GAIN WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                          16    62
  XP GAIN WILD-TYPE                        45   142
D39V11, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                     16                45
  WHITE                                         62               142
[1] 4 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
  XP GAIN MUTATED     4  74
  XP GAIN WILD-TYPE   8 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      4   74
  XP GAIN WILD-TYPE    8  166
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO              74               166
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    79  11
  XQ GAIN WILD-TYPE 162  33
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               90               195 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               11                33 
$`XQ GAIN MUTATED`
TCGA-2Z-A9JQ TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A44B 
       25.58        76.64        21.67        21.07        10.16        11.87 
TCGA-BQ-7046 TCGA-DW-5561 TCGA-DW-7836 TCGA-GL-A59T TCGA-HE-A5NF TCGA-PJ-A5Z9 
       96.92        13.61        35.93        17.95        84.89        17.75 
TCGA-UZ-A9PO TCGA-Y8-A895 TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       62.83        15.91        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 
       56.91        49.58        22.26        78.64        71.80        62.93 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A48D 
       23.97        23.31         0.76        19.63        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 TCGA-AT-A5NU 
       16.96        16.31        15.75        12.46        49.32         2.20 
TCGA-B1-A47N TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4116 TCGA-B9-4117 
       36.49        30.58        50.50        28.18        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5887 
        1.15        43.99         0.16        17.49        47.80        25.35 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 
        0.95         7.92        48.26         7.04         3.81        40.77 
TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A4TM 
       51.19         2.40         1.18        51.78        39.25        25.25 
TCGA-G7-A8LB TCGA-GL-6846 TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NI TCGA-HE-A5NJ 
       17.98       194.79        81.93        58.19        11.84        56.75 
TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       25.22        18.41        29.10        11.41        34.29        27.78 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-SX-A71U TCGA-SX-A71V 
       87.09        99.12        52.27        16.01        44.61        28.80 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK 
       19.00        16.31        41.62        26.47        53.10       117.40 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 

$`XQ GAIN WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        39.88        33.07        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-A5DJ TCGA-B1-A47O TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       49.25        27.68        21.86        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       11.97        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
        3.02        61.02        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A898 TCGA-Y8-A8RZ 
       19.73        41.33        86.37        21.60        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
        7.04         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K3 
        0.13        12.82        11.57       106.55        90.21        15.48 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 
        0.23        16.64        30.48        29.46        25.64        23.28 
TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       19.73         8.48         8.28         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A654 TCGA-B1-A655 
       62.66        67.73        41.13        37.51        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
       20.32        33.83        29.03        34.49        12.46        26.40 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       22.06        17.23        14.86        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 
       26.04        30.28        10.82         7.66         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 
       93.34        61.28        50.40        49.84         7.63         7.17 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       79.86        80.88        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       10.68        13.08         0.43         4.01        90.90        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD 
       71.44        25.15        20.52        25.84        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40U 
       12.89        11.21        16.31        26.01        73.25        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A560 
       21.34        12.36        12.76        10.55        10.09        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       42.94         6.61        92.58        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SU TCGA-UN-AAZ9 
       47.90        49.45        27.06        11.93        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       26.20       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       71.24        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.16              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           194.79            129.86 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            28.49             23.28 
[1] "0.2 - 194.8 (28.5)" "0.1 - 129.9 (23.3)"
[1] "hr=" "1.6"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED        62        7         8        4
  XQ GAIN WILD-TYPE     109       14        44       11
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                62               109
  STAGE II                7                14
  STAGE III               8                44
  STAGE IV                4                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    69  12    11
  XQ GAIN WILD-TYPE 122  21    51
D40V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                 69               122
  T2                 12                21
  T3+T4              11                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                N0 N1 N2
  XQ GAIN MUTATED   12  4  0
  XQ GAIN WILD-TYPE 37 20  4
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              12                37
  N1               4                20
  N2               0                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   27  2
  XQ GAIN WILD-TYPE 67  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     27    2
  XQ GAIN WILD-TYPE   67    7
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              27                67
  1               2                 7
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    16  76
  XQ GAIN WILD-TYPE  60 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     16   76
  XQ GAIN WILD-TYPE   60  136
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              16                60
  MALE                76               136
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
D40V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  2     1
  XQ GAIN WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          18    64
  XQ GAIN WILD-TYPE                        43   140
D40V11, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                     18                43
  WHITE                                         64               140
[1] 4 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
  XQ GAIN MUTATED     4  77
  XQ GAIN WILD-TYPE   8 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4   77
  XQ GAIN WILD-TYPE    8  163
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO              77               163
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    24   6
  1P LOSS WILD-TYPE 217  38
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               30               255 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                38 
$`1P LOSS MUTATED`
TCGA-BQ-7055 TCGA-PJ-A5Z8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9JY 
       26.27        19.73        54.64        51.52        12.82        49.58 
TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 
       15.48        43.04        67.43        18.21         0.10        29.46 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5894 
       37.51        29.03        17.23        86.76        21.63         2.76 
TCGA-BQ-7044 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC 
      123.62        10.68        13.08        25.15        25.84        23.08 
TCGA-GL-8500 TCGA-HE-A5NK TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       27.65        73.25         6.61        14.07        18.02        86.27 

$`1P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       11.97        96.92        44.84        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       67.17        16.34        12.13        29.26        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
        4.57        91.73        56.81        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 
       90.21        22.26        78.64        71.80        62.93        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7732 
       12.99        12.39        27.09        19.63        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
        7.82         0.23        16.64        30.48        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       67.73         2.20        41.13        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
       22.06         0.16        14.86        17.49        12.30        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        7.92        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       11.05        39.25        71.44        20.52        25.25        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92         3.68         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       26.01        11.84        56.75        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.10              0.13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           123.62            194.79 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           25.495            25.280 
[1] "0.1 - 123.6 (25.5)" "0.1 - 194.8 (25.3)"
[1] "hr=" "1.4"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED        11        2         9        2
  1P LOSS WILD-TYPE     160       19        43       13
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                11               160
  STAGE II                2                19
  STAGE III               9                43
  STAGE IV                2                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
  1P LOSS MUTATED    14   5    11
  1P LOSS WILD-TYPE 177  28    51
D41V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                 14               177
  T2                  5                28
  T3+T4              11                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                N0 N1 N2
  1P LOSS MUTATED    3  4  0
  1P LOSS WILD-TYPE 46 20  4
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               3                46
  N1               4                20
  N2               0                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   10  1
  1P LOSS WILD-TYPE 84  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10    1
  1P LOSS WILD-TYPE   84    8
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              10                84
  1               1                 8
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    10  20
  1P LOSS WILD-TYPE  66 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10   20
  1P LOSS WILD-TYPE   66  192
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              10                66
  MALE                20               192
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
D41V10, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                52 
       TCGA-2Z-A9JD        TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-2Z-A9J3        TCGA-2Z-A9J7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-SX-A71S        TCGA-SX-A71U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           8    18
  1P LOSS WILD-TYPE                        53   186
D41V11, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      8                53
  WHITE                                         18               186
[1] 4 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
  1P LOSS MUTATED     1  23
  1P LOSS WILD-TYPE  11 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   23
  1P LOSS WILD-TYPE   11  217
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              23               217
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    19   2
  1Q LOSS WILD-TYPE 222  42
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21               264 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                42 
$`1Q LOSS MUTATED`
TCGA-PJ-A5Z8 TCGA-2Z-A9JG TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9KH TCGA-A4-7286 
       19.73        54.64        12.82        49.58        67.43        18.21 
TCGA-A4-7583 TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5894 
        0.10        37.51        16.77        29.03        17.23         2.76 
TCGA-F9-A7Q0 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-8500 TCGA-HE-A5NK 
       13.08        25.15        25.84        23.08        27.65        73.25 
TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 
        6.61        14.07        18.02 

$`1Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 
       84.89        67.17        16.34        12.13        29.26        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK 
       56.91         4.57        91.73        56.81        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
       11.57       106.55        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       71.80        62.93        43.04        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       27.09        19.63        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 
        2.20        41.13        36.49        20.25        20.32        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 
       20.61         0.46         1.15        43.99        22.06         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        7.92       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       24.89        10.68         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
       51.78        90.90        11.05        39.25        71.44        20.52 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        3.68         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       81.93        58.19        26.01        11.84        56.75        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.09        42.94        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.10              0.13 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            73.25            194.79 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            19.73             25.61 
[1] "0.1 - 73.2 (19.7)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED        10        2         3        2
  1Q LOSS WILD-TYPE     161       19        49       13
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                10               161
  STAGE II                2                19
  STAGE III               3                49
  STAGE IV                2                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
  1Q LOSS MUTATED    13   3     5
  1Q LOSS WILD-TYPE 178  30    57
D42V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1                 13               178
  T2                  3                30
  T3+T4               5                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"
                   vv
clus                N0 N1 N2
  1Q LOSS MUTATED    3  3  0
  1Q LOSS WILD-TYPE 46 21  4
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               3                46
  N1               3                21
  N2               0                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    7  1
  1Q LOSS WILD-TYPE 87  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7    1
  1Q LOSS WILD-TYPE   87    8
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               7                87
  1               1                 8
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     8  13
  1Q LOSS WILD-TYPE  68 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8   13
  1Q LOSS WILD-TYPE   68  199
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               8                68
  MALE                13               199
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                72 
       TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-5P-A9JU        TCGA-B9-A44B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838        TCGA-GL-A59T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-5P-A9K3        TCGA-5P-A9KE        TCGA-A4-8310        TCGA-A4-A48D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-7268        TCGA-B9-A69E        TCGA-DW-7963 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-SX-A71S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D42V10, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                53 
       TCGA-2Z-A9JD        TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-2Z-A9J3        TCGA-2Z-A9J7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-SX-A71S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-WN-A9G9        TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RY 
"1Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           5    13
  1Q LOSS WILD-TYPE                        56   191
D42V11, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      5                56
  WHITE                                         13               191
[1] 4 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
  1Q LOSS MUTATED     1  19
  1Q LOSS WILD-TYPE  11 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   19
  1Q LOSS WILD-TYPE   11  221
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              19               221
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     4   1
  2P LOSS WILD-TYPE 237  43
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               280 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                43 
$`2P LOSS MUTATED`
TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9KH TCGA-BQ-5875 TCGA-HE-7130 
       12.82        15.48        67.43        86.76        58.19 

$`2P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        5.29         0.13        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       22.26        78.64        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.99        12.39        27.09        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
       17.23         0.16        14.86        17.49        12.30        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            12.82              0.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            86.76            194.79 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           58.190            25.265 
[1] "12.8 - 86.8 (58.2)" "0.1 - 194.8 (25.3)"
[1] "hr=" "1.1"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         0        0         2        1
  2P LOSS WILD-TYPE     171       21        50       14
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 0               171
  STAGE II                0                21
  STAGE III               2                50
  STAGE IV                1                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 LOSS MUTATED     1   1     3
  2P LOSS WILD-TYPE 190  32    59
D43V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1                  1               190
  T2                  1                32
  T3+T4               3                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                N0 N1 N2
  2P LOSS MUTATED    0  1  0
  2P LOSS WILD-TYPE 49 23  4
D43V5, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                76 
       TCGA-5P-A9JU        TCGA-A4-A5Y1        TCGA-B1-A47O        TCGA-B1-A657 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5892        TCGA-BQ-7056        TCGA-IA-A83W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-2Z-A9J1        TCGA-2Z-A9JO        TCGA-4A-A93W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-5P-A9K9        TCGA-A4-7583        TCGA-A4-7585 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7915        TCGA-A4-A57E        TCGA-A4-A7UZ        TCGA-AL-3466 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A655        TCGA-B1-A656        TCGA-B9-7268        TCGA-BQ-5877 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5889        TCGA-BQ-5890 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-DW-7963 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-F9-A8NY        TCGA-F9-A97G        TCGA-G7-6789 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-6846        TCGA-GL-7966        TCGA-GL-A59R        TCGA-GL-A9DC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720        TCGA-J7-8537 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-J7-A8I2        TCGA-KV-A74V        TCGA-P4-A5E6        TCGA-P4-A5E8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-A5EA        TCGA-P4-AAVK        TCGA-P4-AAVL        TCGA-SX-A71R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SP        TCGA-SX-A7SS        TCGA-UN-AAZ9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PQ        TCGA-UZ-A9PX        TCGA-Y8-A897 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    2  0
  2P LOSS WILD-TYPE 92  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    0
  2P LOSS WILD-TYPE   92    9
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               2                92
  1               0                 9
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2   3
  2P LOSS WILD-TYPE  74 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    3
  2P LOSS WILD-TYPE   74  209
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                74
  MALE                 3               209
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                75 
       TCGA-2Z-A9JL        TCGA-2Z-A9JT        TCGA-5P-A9JU        TCGA-DW-5560 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-2Z-A9JE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JK        TCGA-2Z-A9JN        TCGA-4A-A93W        TCGA-4A-A93Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F9-A7Q0        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537        TCGA-P4-AAVK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SU        TCGA-UZ-A9PL        TCGA-V9-A7HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V9, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                73 
       TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-5P-A9JU        TCGA-B9-A44B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838        TCGA-GL-A59T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-5P-A9KE        TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4117 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A8RY 
"2P LOSS WILD-TYPE" 
D43V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0     4
  2P LOSS WILD-TYPE                        61   200
D43V11, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                61
  WHITE                                          4               200
[1] 4 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
  2P LOSS MUTATED     0   3
  2P LOSS WILD-TYPE  12 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    3
  2P LOSS WILD-TYPE   12  237
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               3               237
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     3   0
  2Q LOSS WILD-TYPE 238  44
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3               282 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                44 
$`2Q LOSS MUTATED`
TCGA-4A-A93X TCGA-5P-A9KH TCGA-HE-7130 
       12.82        67.43        58.19 

$`2Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        5.29         0.13        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 
       19.36        12.99        12.39        27.09        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            12.82              0.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            67.43            194.79 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           58.190            25.265 
[1] "12.8 - 67.4 (58.2)" "0.1 - 194.8 (25.3)"
[1] "hr="     "9200000"
D44V2, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               281 
       TCGA-2Z-A9J9        TCGA-2Z-A9JD        TCGA-2Z-A9JJ        TCGA-2Z-A9JL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JQ        TCGA-2Z-A9JS        TCGA-2Z-A9JT        TCGA-5P-A9JU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5P-A9JV        TCGA-A4-7288        TCGA-A4-7584        TCGA-A4-7734 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-A5Y1        TCGA-AL-3468        TCGA-AL-A5DJ        TCGA-B1-A47M 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B1-A47O        TCGA-B1-A657        TCGA-B3-A6W5        TCGA-B9-5155 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W7        TCGA-BQ-5886        TCGA-BQ-5888 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-7046        TCGA-BQ-7049        TCGA-BQ-7055 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DW-5560        TCGA-DW-5561 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-GL-A59T        TCGA-HE-A5NF        TCGA-IA-A83W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-MH-A855        TCGA-MH-A857        TCGA-PJ-A5Z8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-SX-A7SO        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PZ        TCGA-Y8-A895        TCGA-Y8-A898        TCGA-Y8-A8RZ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2K-A9WE        TCGA-2Z-A9J1        TCGA-2Z-A9J2        TCGA-2Z-A9J3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J5        TCGA-2Z-A9J6        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JE        TCGA-2Z-A9JG        TCGA-2Z-A9JI        TCGA-2Z-A9JK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JM        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JR        TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-5P-A9JW 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5P-A9JY        TCGA-5P-A9JZ        TCGA-5P-A9K0        TCGA-5P-A9K2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5P-A9K3        TCGA-5P-A9K4        TCGA-5P-A9K6        TCGA-5P-A9K8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5P-A9K9        TCGA-5P-A9KA        TCGA-5P-A9KC        TCGA-5P-A9KE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7583        TCGA-A4-7585 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-7732        TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-7997        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A5Y0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-A6HP        TCGA-A4-A772        TCGA-A4-A7UZ        TCGA-AL-3466 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AL-3467        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-AT-A5NU        TCGA-B1-5398        TCGA-B1-7332 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B1-A47N        TCGA-B1-A654        TCGA-B1-A655        TCGA-B1-A656 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B3-8121        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-B9-A69E 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-A8YH        TCGA-B9-A8YI        TCGA-BQ-5875        TCGA-BQ-5876 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5889        TCGA-BQ-5890 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7062        TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-F9-A4JJ        TCGA-F9-A7Q0        TCGA-F9-A7VF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F9-A8NY        TCGA-F9-A97G        TCGA-G7-6789        TCGA-G7-6790 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GL-6846        TCGA-GL-7773        TCGA-GL-7966        TCGA-GL-8500 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A9DC        TCGA-GL-A9DD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GL-A9DE        TCGA-HE-A5NH        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HE-A5NK        TCGA-HE-A5NL        TCGA-IA-A40U        TCGA-IA-A40X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-IA-A83S        TCGA-IA-A83T        TCGA-IA-A83V 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IZ-8195        TCGA-IZ-8196        TCGA-IZ-A6M9        TCGA-J7-6720 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-J7-8537        TCGA-J7-A8I2        TCGA-KV-A6GD        TCGA-KV-A6GE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KV-A74V        TCGA-MH-A55W        TCGA-MH-A55Z        TCGA-MH-A560 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MH-A561        TCGA-MH-A562        TCGA-MH-A854        TCGA-MH-A856 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-O9-A75Z        TCGA-P4-A5E6        TCGA-P4-A5E7        TCGA-P4-A5E8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-P4-A5EA        TCGA-P4-A5EB        TCGA-P4-A5ED        TCGA-P4-AAVK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-P4-AAVL        TCGA-P4-AAVM        TCGA-P4-AAVO        TCGA-Q2-A5QZ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UN-AAZ9        TCGA-UZ-A9PJ        TCGA-UZ-A9PK        TCGA-UZ-A9PL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PN        TCGA-UZ-A9PP        TCGA-UZ-A9PQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PS        TCGA-UZ-A9PU        TCGA-UZ-A9PV        TCGA-UZ-A9PX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9Q0        TCGA-UZ-A9Q1        TCGA-V9-A7HT        TCGA-Y8-A894 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A897        TCGA-Y8-A8RY        TCGA-Y8-A8S0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Y8-A8S1 
"2Q LOSS WILD-TYPE" 
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         0        0         1        1
  2Q LOSS WILD-TYPE     171       21        51       14
D44V3, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               257 
       TCGA-2Z-A9J9        TCGA-2Z-A9JD        TCGA-2Z-A9JJ        TCGA-2Z-A9JL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JQ        TCGA-2Z-A9JS        TCGA-2Z-A9JT        TCGA-5P-A9JU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7734        TCGA-A4-A5Y1        TCGA-AL-3468 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AL-A5DJ        TCGA-B1-A47M        TCGA-B1-A47O        TCGA-B1-A657 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B3-A6W5        TCGA-B9-5155        TCGA-B9-A44B        TCGA-B9-A5W7 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5888        TCGA-BQ-5892        TCGA-BQ-7046 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7049        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6134        TCGA-GL-A59T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HE-A5NF        TCGA-IA-A83W        TCGA-IZ-A6M8        TCGA-MH-A855 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MH-A857        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9        TCGA-SX-A7SO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-UZ-A9PZ        TCGA-Y8-A895 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Y8-A898        TCGA-Y8-A8RZ        TCGA-2K-A9WE        TCGA-2Z-A9J1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J2        TCGA-2Z-A9J3        TCGA-2Z-A9J5        TCGA-2Z-A9J6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JE        TCGA-2Z-A9JG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM        TCGA-2Z-A9JN 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JO        TCGA-2Z-A9JP        TCGA-2Z-A9JR        TCGA-4A-A93W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-7287        TCGA-A4-7583        TCGA-A4-7585 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A5Y0        TCGA-A4-A6HP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-A772        TCGA-A4-A7UZ        TCGA-AL-3466        TCGA-AL-3471 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AL-3473        TCGA-AL-7173        TCGA-AT-A5NU        TCGA-B1-5398 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B1-7332        TCGA-B1-A47N        TCGA-B1-A654        TCGA-B1-A655 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B1-A656        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113        TCGA-B9-4115 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-B9-A69E 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-A8YH        TCGA-B9-A8YI        TCGA-BQ-5875        TCGA-BQ-5876 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5889        TCGA-BQ-5890 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7062        TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-F9-A4JJ        TCGA-F9-A7Q0        TCGA-F9-A7VF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F9-A8NY        TCGA-F9-A97G        TCGA-G7-6789        TCGA-G7-6790 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GL-6846        TCGA-GL-7773        TCGA-GL-7966        TCGA-GL-8500 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A9DC        TCGA-GL-A9DD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GL-A9DE        TCGA-HE-7128        TCGA-HE-7129        TCGA-HE-A5NH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NL        TCGA-IA-A40U        TCGA-IA-A40X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-IA-A83V        TCGA-IZ-8195        TCGA-IZ-8196 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IZ-A6M9        TCGA-J7-6720        TCGA-J7-8537        TCGA-J7-A8I2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KV-A6GD        TCGA-KV-A6GE        TCGA-KV-A74V        TCGA-MH-A55W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MH-A55Z        TCGA-MH-A560        TCGA-MH-A561        TCGA-MH-A562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A856        TCGA-O9-A75Z        TCGA-P4-A5E6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5E8        TCGA-P4-A5EA        TCGA-P4-A5EB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-P4-A5ED        TCGA-P4-AAVK        TCGA-P4-AAVL        TCGA-P4-AAVM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-P4-AAVO        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-SX-A7SU        TCGA-UN-AAZ9        TCGA-UZ-A9PJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PK        TCGA-UZ-A9PL        TCGA-UZ-A9PM        TCGA-UZ-A9PN 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PP        TCGA-UZ-A9PQ        TCGA-UZ-A9PS        TCGA-UZ-A9PU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PV        TCGA-UZ-A9PX        TCGA-UZ-A9Q0        TCGA-UZ-A9Q1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-V9-A7HT        TCGA-WN-A9G9        TCGA-WN-AB4C        TCGA-Y8-A894 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A897        TCGA-Y8-A8RY        TCGA-Y8-A8S0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Y8-A8S1 
"2Q LOSS WILD-TYPE" 
                   vv
clus                 T1  T2 T3+T4
  2Q LOSS MUTATED     1   0     2
  2Q LOSS WILD-TYPE 190  33    60
D44V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1                  1               190
  T2                  0                33
  T3+T4               2                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                N0 N1 N2
  2Q LOSS MUTATED    0  1  0
  2Q LOSS WILD-TYPE 49 23  4
D44V5, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                76 
       TCGA-5P-A9JU        TCGA-A4-A5Y1        TCGA-B1-A47O        TCGA-B1-A657 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5892        TCGA-BQ-7056        TCGA-IA-A83W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-2Z-A9J1        TCGA-2Z-A9JO        TCGA-4A-A93W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-5P-A9K9        TCGA-A4-7583        TCGA-A4-7585 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-7915        TCGA-A4-A57E        TCGA-A4-A7UZ        TCGA-AL-3466 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B1-A655        TCGA-B1-A656        TCGA-B9-7268        TCGA-BQ-5877 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5889        TCGA-BQ-5890 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-DW-7963 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-F9-A8NY        TCGA-F9-A97G        TCGA-G7-6789 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GL-6846        TCGA-GL-7966        TCGA-GL-A59R        TCGA-GL-A9DC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720        TCGA-J7-8537 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-J7-A8I2        TCGA-KV-A74V        TCGA-P4-A5E6        TCGA-P4-A5E8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-P4-A5EA        TCGA-P4-AAVK        TCGA-P4-AAVL        TCGA-SX-A71R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SP        TCGA-SX-A7SS        TCGA-UN-AAZ9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PQ        TCGA-UZ-A9PX        TCGA-Y8-A897 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D44V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    1  0
  2Q LOSS WILD-TYPE 93  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    0
  2Q LOSS WILD-TYPE   93    9
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               1                93
  1               0                 9
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1   2
  2Q LOSS WILD-TYPE  75 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    2
  2Q LOSS WILD-TYPE   75  210
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               1                75
  MALE                 2               210
[1] 2 2
[1] FALSE
D44V8, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                75 
       TCGA-2Z-A9JL        TCGA-2Z-A9JT        TCGA-5P-A9JU        TCGA-DW-5560 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-2Z-A9JE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JK        TCGA-2Z-A9JN        TCGA-4A-A93W        TCGA-4A-A93Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F9-A7Q0        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537        TCGA-P4-AAVK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A7SU        TCGA-UZ-A9PL        TCGA-V9-A7HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D44V9, continuous
D44V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     0
  2Q LOSS WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           0     2
  2Q LOSS WILD-TYPE                        61   202
D44V11, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               271 
       TCGA-2Z-A9J9        TCGA-2Z-A9JD        TCGA-2Z-A9JJ        TCGA-2Z-A9JL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JQ        TCGA-2Z-A9JS        TCGA-2Z-A9JT        TCGA-5P-A9JU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5P-A9JV        TCGA-A4-7288        TCGA-A4-7584        TCGA-A4-7734 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-A5Y1        TCGA-AL-3468        TCGA-AL-A5DJ        TCGA-B1-A47M 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B1-A47O        TCGA-B1-A657        TCGA-B3-A6W5        TCGA-B9-5155 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W7        TCGA-BQ-5886        TCGA-BQ-5888 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-7046        TCGA-BQ-7049        TCGA-BQ-7055 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DW-5560        TCGA-DW-5561 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-GL-A59T        TCGA-IA-A83W        TCGA-IZ-A6M8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MH-A855        TCGA-MH-A857        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A7SO        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-UZ-A9PZ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Y8-A895        TCGA-Y8-A898        TCGA-Y8-A8RZ        TCGA-2K-A9WE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J1        TCGA-2Z-A9J2        TCGA-2Z-A9J3        TCGA-2Z-A9J5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J6        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JG        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JP        TCGA-2Z-A9JR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-5P-A9JW        TCGA-5P-A9JY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5P-A9JZ        TCGA-5P-A9K0        TCGA-5P-A9K2        TCGA-5P-A9K3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5P-A9K4        TCGA-5P-A9K6        TCGA-5P-A9K8        TCGA-5P-A9K9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5P-A9KA        TCGA-5P-A9KC        TCGA-5P-A9KE        TCGA-A4-7286 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-7287        TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7732 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A5Y0        TCGA-A4-A6HP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A4-A772        TCGA-A4-A7UZ        TCGA-AL-3466        TCGA-AL-3467 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AT-A5NU        TCGA-B1-5398        TCGA-B1-7332        TCGA-B1-A47N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B1-A654        TCGA-B1-A655        TCGA-B1-A656        TCGA-B3-3925 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5156        TCGA-B9-7268 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-B9-A69E        TCGA-B9-A8YH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B9-A8YI        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5887 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5893 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7059        TCGA-BQ-7060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-7963        TCGA-DZ-6131 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F9-A4JJ        TCGA-F9-A7Q0        TCGA-F9-A7VF        TCGA-F9-A8NY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-6846 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-7966        TCGA-GL-8500        TCGA-GL-A4EM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GL-A59R        TCGA-GL-A9DC        TCGA-GL-A9DD        TCGA-GL-A9DE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IA-A83S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IA-A83T        TCGA-IA-A83V        TCGA-IZ-8195        TCGA-IZ-8196 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IZ-A6M9        TCGA-J7-6720        TCGA-J7-8537        TCGA-J7-A8I2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KV-A6GD        TCGA-KV-A6GE        TCGA-KV-A74V        TCGA-MH-A55W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MH-A55Z        TCGA-MH-A560        TCGA-MH-A561        TCGA-MH-A562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A856        TCGA-O9-A75Z        TCGA-P4-A5E6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5E8        TCGA-P4-A5EA        TCGA-P4-A5EB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-P4-A5ED        TCGA-P4-AAVK        TCGA-P4-AAVL        TCGA-P4-AAVM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-P4-AAVO        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SM        TCGA-SX-A7SN 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UN-AAZ9        TCGA-UZ-A9PJ        TCGA-UZ-A9PK        TCGA-UZ-A9PL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PN        TCGA-UZ-A9PP        TCGA-UZ-A9PQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PS        TCGA-UZ-A9PU        TCGA-UZ-A9PV        TCGA-UZ-A9PX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UZ-A9Q0        TCGA-UZ-A9Q1        TCGA-V9-A7HT        TCGA-WN-A9G9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A897 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RY        TCGA-Y8-A8S0        TCGA-Y8-A8S1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D44V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   2
  2Q LOSS WILD-TYPE  12 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    2
  2Q LOSS WILD-TYPE   12  238
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               2               238
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    14   7
  3P LOSS WILD-TYPE 227  37
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21               264 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                37 
$`3P LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-BQ-5892 TCGA-Y8-A8RZ TCGA-2Z-A9JG TCGA-2Z-A9JI 
       12.99        11.87        11.97         6.74        54.64        51.52 
TCGA-2Z-A9JK TCGA-A4-A57E TCGA-AL-3473 TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5882 
       38.99         8.48        62.66        14.86         8.88        21.63 
TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 
       79.86         4.01        23.08         3.68         2.04        10.55 
TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-WN-A9G9 
       14.07        86.27        26.01 

$`3P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 
       21.86        19.23        26.04        13.25        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-2K-A9WE TCGA-2Z-A9J1 
       86.37        21.60        15.91        15.62         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       56.81        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
       16.96        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        49.32        66.71        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       17.23         0.16        17.49        12.30        86.76        19.27 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       10.68        13.08         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 
       96.69        22.26        21.34        12.36        12.76        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C 
       47.47        65.13       110.73        51.35        31.73        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2.04              0.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            86.27            194.79 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            14.07             25.74 
[1] "2.0 - 86.3 (14.1)"  "0.1 - 194.8 (25.7)"
[1] "hr=" "3.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         5        1        12        3
  3P LOSS WILD-TYPE     166       20        40       12
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 5               166
  STAGE II                1                20
  STAGE III              12                40
  STAGE IV                3                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
  3P LOSS MUTATED     6   3    12
  3P LOSS WILD-TYPE 185  30    50
D45V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  6               185
  T2                  3                30
  T3+T4              12                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                N0 N1 N2
  3P LOSS MUTATED    6  6  1
  3P LOSS WILD-TYPE 43 18  3
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               6                43
  N1               6                18
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    4  2
  3P LOSS WILD-TYPE 90  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    2
  3P LOSS WILD-TYPE   90    7
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               4                90
  1               2                 7
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     5  16
  3P LOSS WILD-TYPE  71 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5   16
  3P LOSS WILD-TYPE   71  196
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                71
  MALE                16               196
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
D45V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     1
  3P LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           4    15
  3P LOSS WILD-TYPE                        57   189
D45V11, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      4                57
  WHITE                                         15               189
[1] 4 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
  3P LOSS MUTATED     0  18
  3P LOSS WILD-TYPE  12 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   18
  3P LOSS WILD-TYPE   12  222
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              18               222
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     3   3
  3Q LOSS WILD-TYPE 238  41
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               279 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                41 
$`3Q LOSS MUTATED`
TCGA-2Z-A9JG TCGA-BQ-5877 TCGA-BQ-5882 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7966 
       54.64         8.88        21.63         4.01        23.08         3.68 

$`3Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI 
      100.27        56.91         4.57        91.73        56.81        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76        19.27        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       47.80        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.98        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             3.68              0.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            54.64            194.79 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           15.255            25.580 
[1] "3.7 - 54.6 (15.3)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "6.3"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         2        0         2        2
  3Q LOSS WILD-TYPE     169       21        50       13
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 2               169
  STAGE II                0                21
  STAGE III               2                50
  STAGE IV                2                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 LOSS MUTATED     2   0     4
  3Q LOSS WILD-TYPE 189  33    58
D46V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                  2               189
  T2                  0                33
  T3+T4               4                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"
                   vv
clus                N0 N1 N2
  3Q LOSS MUTATED    1  2  1
  3Q LOSS WILD-TYPE 48 22  3
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               1                48
  N1               2                22
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  1
  3Q LOSS WILD-TYPE 93  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    1
  3Q LOSS WILD-TYPE   93    8
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               1                93
  1               1                 8
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2   4
  3Q LOSS WILD-TYPE  74 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    4
  3Q LOSS WILD-TYPE   74  208
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                74
  MALE                 4               208
[1] 2 2
[1] FALSE
D46V8, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                74 
       TCGA-2Z-A9JL        TCGA-2Z-A9JT        TCGA-5P-A9JU        TCGA-DW-5560 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-2Z-A9JE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JK        TCGA-2Z-A9JN        TCGA-4A-A93W        TCGA-4A-A93X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-F9-A7Q0        TCGA-G7-6790        TCGA-G7-6792 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-J7-8537        TCGA-P4-AAVK        TCGA-Q2-A5QZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PL        TCGA-V9-A7HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D46V9, continuous
D46V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1     4
  3Q LOSS WILD-TYPE                        60   200
D46V11, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                60
  WHITE                                          4               200
[1] 4 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
  3Q LOSS MUTATED     0   4
  3Q LOSS WILD-TYPE  12 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    4
  3Q LOSS WILD-TYPE   12  236
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               4               236
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    13  12
  4P LOSS WILD-TYPE 228  32
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               25               260 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               12                32 
$`4P LOSS MUTATED`
TCGA-AL-A5DJ TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-A4-7287 
       49.25        51.52        12.82        15.48        19.36        19.63 
TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-DZ-6131 
       37.51        29.03        22.92        21.63         2.76        79.86 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-7130 
       10.68        13.08        20.52        16.90         3.68        58.19 
TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-Q2-A5QZ 
       73.25         2.04        10.55        42.94         6.61        14.07 
TCGA-UN-AAZ9 
       18.02 

$`4P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK 
       56.91         4.57        91.73        56.81        54.64        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       67.43        18.21         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       67.73         2.20        41.13        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        63.72        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        0.95         7.92       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       40.77        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       24.89         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 
       90.90        11.05        39.25        71.44        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        23.08        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       81.93        26.01        11.84        56.75        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
       31.13        15.48        99.78        87.09        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2.04              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            79.86            194.79 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           19.360            25.925 
[1] "2.0 - 79.9 (19.4)"  "0.1 - 194.8 (25.9)"
[1] "hr=" "5.8"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         4        1        15        2
  4P LOSS WILD-TYPE     167       20        37       13
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 4               167
  STAGE II                1                20
  STAGE III              15                37
  STAGE IV                2                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     5   3    17
  4P LOSS WILD-TYPE 186  30    45
D47V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                  5               186
  T2                  3                30
  T3+T4              17                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                N0 N1 N2
  4P LOSS MUTATED    3 10  1
  4P LOSS WILD-TYPE 46 14  3
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0               3                46
  N1              10                14
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    8  1
  4P LOSS WILD-TYPE 86  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8    1
  4P LOSS WILD-TYPE   86    8
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               8                86
  1               1                 8
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    16   9
  4P LOSS WILD-TYPE  60 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16    9
  4P LOSS WILD-TYPE   60  203
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              16                60
  MALE                 9               203
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           5    14
  4P LOSS WILD-TYPE                        56   190
D47V11, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      5                56
  WHITE                                         14               190
[1] 4 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
  4P LOSS MUTATED     1  18
  4P LOSS WILD-TYPE  11 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   18
  4P LOSS WILD-TYPE   11  222
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              18               222
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    14  12
  4Q LOSS WILD-TYPE 227  32
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               26               259 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               12                32 
$`4Q LOSS MUTATED`
TCGA-AL-A5DJ TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-A4-7287 
       49.25        51.52        12.82        15.48        19.36        19.63 
TCGA-A4-A57E TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-BQ-5894 
        8.48        37.51        29.03        19.27        21.63         2.76 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 
       79.86        10.68        13.08        20.52        16.90         3.68 
TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 TCGA-P4-A5EA 
       58.19        73.25         2.04        10.55        42.94         6.61 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       14.07        18.02 

$`4Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK 
       56.91         4.57        91.73        56.81        54.64        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       67.43        18.21         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       12.46        16.96        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
        2.20        41.13        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       33.83        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        7.92       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
       11.05        39.25        71.44        25.15        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.98        23.08        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       26.01        11.84        56.75        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       15.48        99.78        87.09        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2.04              0.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            79.86            194.79 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           18.645            26.010 
[1] "2.0 - 79.9 (18.6)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "5.9"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         5        1        14        3
  4Q LOSS WILD-TYPE     166       20        38       12
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 5               166
  STAGE II                1                20
  STAGE III              14                38
  STAGE IV                3                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     6   4    16
  4Q LOSS WILD-TYPE 185  29    46
D48V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                  6               185
  T2                  4                29
  T3+T4              16                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"
                   vv
clus                N0 N1 N2
  4Q LOSS MUTATED    4  9  1
  4Q LOSS WILD-TYPE 45 15  3
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0               4                45
  N1               9                15
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    8  2
  4Q LOSS WILD-TYPE 86  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8    2
  4Q LOSS WILD-TYPE   86    7
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               8                86
  1               2                 7
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    15  11
  4Q LOSS WILD-TYPE  61 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     15   11
  4Q LOSS WILD-TYPE   61  201
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              15                61
  MALE                11               201
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
D48V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           5    15
  4Q LOSS WILD-TYPE                        56   189
D48V11, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      5                56
  WHITE                                         15               189
[1] 4 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
  4Q LOSS MUTATED     1  19
  4Q LOSS WILD-TYPE  11 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   19
  4Q LOSS WILD-TYPE   11  221
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              19               221
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     3   4
  5P LOSS WILD-TYPE 238  40
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               278 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                40 
$`5P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7997 TCGA-BQ-5879 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-G7-6793 
       18.21        30.48        22.92         2.76        10.68        11.05 
TCGA-P4-A5EA 
        6.61 

$`5P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        63.72        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         0.95         7.92       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        24.89        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        0.43         4.01        51.78        90.90        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.09        42.94        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2.76              0.10 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            30.48            194.79 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            11.05             25.61 
[1] "2.8 - 30.5 (11.1)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "12" 
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         1        0         3        2
  5P LOSS WILD-TYPE     170       21        49       13
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 1               170
  STAGE II                0                21
  STAGE III               3                49
  STAGE IV                2                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
  5P LOSS MUTATED     1   0     6
  5P LOSS WILD-TYPE 190  33    56
D49V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                  1               190
  T2                  0                33
  T3+T4               6                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"
                   vv
clus                N0 N1 N2
  5P LOSS MUTATED    0  3  1
  5P LOSS WILD-TYPE 49 21  3
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0               0                49
  N1               3                21
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  1
  5P LOSS WILD-TYPE 92  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    1
  5P LOSS WILD-TYPE   92    8
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               2                92
  1               1                 8
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4   3
  5P LOSS WILD-TYPE  72 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    3
  5P LOSS WILD-TYPE   72  209
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               4                72
  MALE                 3               209
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                74 
       TCGA-2Z-A9JL        TCGA-2Z-A9JT        TCGA-5P-A9JU        TCGA-DW-5560 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-2Z-A9JE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-2Z-A9JK        TCGA-2Z-A9JN        TCGA-4A-A93W        TCGA-4A-A93X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F9-A7Q0        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-J7-8537        TCGA-P4-AAVK        TCGA-Q2-A5QZ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-UZ-A9PL        TCGA-V9-A7HT 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D49V9, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                73 
       TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-5P-A9JU        TCGA-B9-A44B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838        TCGA-GL-A59T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-5P-A9K3        TCGA-5P-A9KE        TCGA-A4-8310        TCGA-A4-A48D 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-7268        TCGA-B9-A69E        TCGA-DW-7963 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6792        TCGA-G7-6795        TCGA-G7-7501 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-Y8-A8RY 
"5P LOSS WILD-TYPE" 
D49V10, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                53 
       TCGA-2Z-A9JD        TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-2Z-A9J3        TCGA-2Z-A9J7 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-WN-A9G9        TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-Y8-A8RY 
"5P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1     5
  5P LOSS WILD-TYPE                        60   199
D49V11, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                60
  WHITE                                          5               199
[1] 4 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
  5P LOSS MUTATED     1   4
  5P LOSS WILD-TYPE  11 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    4
  5P LOSS WILD-TYPE   11  236
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               4               236
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     4   4
  5Q LOSS WILD-TYPE 237  40
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8               277 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                40 
$`5Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7997 TCGA-BQ-5879 TCGA-BQ-5894 TCGA-F9-A4JJ 
       18.21        19.63        30.48        22.92         2.76        10.68 
TCGA-GL-7966 TCGA-P4-A5EA 
        3.68         6.61 

$`5Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27         8.88        63.72        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        0.95         7.92       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       19.00        24.89        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.76              0.10 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            30.48            194.79 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           14.445            25.640 
[1] "2.8 - 30.5 (14.4)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "10" 
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         2        0         4        1
  5Q LOSS WILD-TYPE     169       21        48       14
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 2               169
  STAGE II                0                21
  STAGE III               4                48
  STAGE IV                1                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
  5Q LOSS MUTATED     2   0     6
  5Q LOSS WILD-TYPE 189  33    56
D50V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  2               189
  T2                  0                33
  T3+T4               6                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"
                   vv
clus                N0 N1 N2
  5Q LOSS MUTATED    0  4  0
  5Q LOSS WILD-TYPE 49 20  4
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               0                49
  N1               4                20
  N2               0                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2  1
  5Q LOSS WILD-TYPE 92  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    1
  5Q LOSS WILD-TYPE   92    8
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               2                92
  1               1                 8
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5   3
  5Q LOSS WILD-TYPE  71 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    3
  5Q LOSS WILD-TYPE   71  209
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               5                71
  MALE                 3               209
[1] 2 2
[1] FALSE
D50V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                75 
       TCGA-2Z-A9JL        TCGA-2Z-A9JT        TCGA-5P-A9JU        TCGA-DW-5560 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-2Z-A9JE 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JK        TCGA-2Z-A9JN        TCGA-4A-A93W        TCGA-4A-A93X 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F9-A7Q0        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537        TCGA-P4-AAVK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A7SU        TCGA-UZ-A9PL        TCGA-V9-A7HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D50V9, continuous
D50V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     0
  5Q LOSS WILD-TYPE                                2     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1     6
  5Q LOSS WILD-TYPE                        60   198
D50V11, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                60
  WHITE                                          6               198
[1] 4 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
  5Q LOSS MUTATED     1   5
  5Q LOSS WILD-TYPE  11 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    5
  5Q LOSS WILD-TYPE   11  235
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               5               235
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    17   4
  6P LOSS WILD-TYPE 224  40
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               21               264 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4                40 
$`6P LOSS MUTATED`
TCGA-5P-A9JU TCGA-BQ-7056 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-5P-A9KH TCGA-A4-7286 
       12.26        20.12        54.64        51.52        67.43        18.21 
TCGA-B3-3926 TCGA-BQ-5882 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       29.03        21.63        19.00        13.08         4.01        11.05 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-7130 TCGA-P4-A5E8 
       25.15        25.84        23.08         3.68        58.19        42.94 
TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-Y8-A896 
       27.06        18.02        18.64 

$`6P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       22.49        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       96.92        44.84        26.27        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
        4.57        91.73        56.81        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       71.80        62.93        43.04        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       27.09        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       16.77        20.32        33.83        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       51.19        74.60        34.19        24.89        10.68         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        1.18         0.43        51.78        90.90        39.25        71.44 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       20.52        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       44.61        28.80        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       39.06        18.64        18.05        25.28         6.02        13.28 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             3.68              0.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            67.43            194.79 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            21.63             25.61 
[1] "3.7 - 67.4 (21.6)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "1.7"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         8        0         9        2
  6P LOSS WILD-TYPE     163       21        43       13
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 8               163
  STAGE II                0                21
  STAGE III               9                43
  STAGE IV                2                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
  6P LOSS MUTATED    10   1    10
  6P LOSS WILD-TYPE 181  32    52
D51V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                 10               181
  T2                  1                32
  T3+T4              10                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"
                   vv
clus                N0 N1 N2
  6P LOSS MUTATED    4  2  2
  6P LOSS WILD-TYPE 45 22  2
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0               4                45
  N1               2                22
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    9  0
  6P LOSS WILD-TYPE 85  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9    0
  6P LOSS WILD-TYPE   85    9
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               9                85
  1               0                 9
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     8  13
  6P LOSS WILD-TYPE  68 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      8   13
  6P LOSS WILD-TYPE   68  199
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               8                68
  MALE                13               199
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
D51V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     1
  6P LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           1    16
  6P LOSS WILD-TYPE                        60   188
D51V11, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      1                60
  WHITE                                         16               188
[1] 4 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
  6P LOSS MUTATED     0  17
  6P LOSS WILD-TYPE  12 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   17
  6P LOSS WILD-TYPE   12  223
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              17               223
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    22   5
  6Q LOSS WILD-TYPE 219  39
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               27               258 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5                39 
$`6Q LOSS MUTATED`
TCGA-2Z-A9JJ TCGA-5P-A9JU TCGA-B9-A44B TCGA-BQ-5888 TCGA-BQ-7056 TCGA-2Z-A9J8 
       39.88        12.26        11.87        13.25        20.12        91.73 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-5P-A9KH TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-5875 
       54.64        51.52        67.43        18.21        29.03        86.76 
TCGA-BQ-5882 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 
       21.63        19.00        13.08         4.01        11.05        25.84 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-7130 TCGA-J7-8537 TCGA-P4-A5EB TCGA-SX-A7SL 
       23.08         3.68        58.19        10.55        99.12        27.06 
TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       18.02        86.27        18.64 

$`6Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        33.07        25.58        16.18        22.49 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       19.23        26.04        11.97        96.92        44.84        26.27 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JK 
       58.22       100.27        56.91         4.57        56.81        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       12.99        12.39        27.09        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
       36.49        20.25        16.77        20.32        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        12.30        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
       80.88        51.19        74.60        34.19        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        2.40         1.18         0.43        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       71.44        25.15        20.52        25.25        17.98        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       49.45        44.61        28.80        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       39.06        18.64        18.05        25.28         6.02        13.28 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             3.68              0.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            99.12            194.79 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           21.630            25.465 
[1] "3.7 - 99.1 (21.6)"  "0.1 - 194.8 (25.5)"
[1] "hr=" "1.2"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED        12        0        11        2
  6Q LOSS WILD-TYPE     159       21        41       13
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                12               159
  STAGE II                0                21
  STAGE III              11                41
  STAGE IV                2                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
  6Q LOSS MUTATED    13   1    13
  6Q LOSS WILD-TYPE 178  32    49
D52V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                 13               178
  T2                  1                32
  T3+T4              13                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                N0 N1 N2
  6Q LOSS MUTATED    5  3  2
  6Q LOSS WILD-TYPE 44 21  2
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0               5                44
  N1               3                21
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   12  0
  6Q LOSS WILD-TYPE 82  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12    0
  6Q LOSS WILD-TYPE   82    9
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              12                82
  1               0                 9
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    12  15
  6Q LOSS WILD-TYPE  64 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12   15
  6Q LOSS WILD-TYPE   64  197
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              12                64
  MALE                15               197
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
D52V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     2
  6Q LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    19
  6Q LOSS WILD-TYPE                        58   185
D52V11, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      3                58
  WHITE                                         19               185
[1] 4 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
  6Q LOSS MUTATED     0  21
  6Q LOSS WILD-TYPE  12 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   21
  6Q LOSS WILD-TYPE   12  219
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              21               219
[1] 2 2
[1] FALSE

Clustering(53) Variable = 8P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    10   6
  8P LOSS WILD-TYPE 231  38
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16               269 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6                38 
$`8P LOSS MUTATED`
TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-DW-5560 TCGA-SX-A7SO TCGA-2Z-A9J3 TCGA-5P-A9K3 
       67.17        12.99        48.85        41.33        58.22        15.48 
TCGA-5P-A9K8 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5889 TCGA-F9-A7Q0 
       43.04         9.63        37.51        29.03        10.82        13.08 
TCGA-F9-A8NY TCGA-G7-A8LC TCGA-G7-A8LD TCGA-UN-AAZ9 
        1.18        23.08        16.90        18.02 

$`8P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       22.49        12.26        61.05        21.37         0.89        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5561 TCGA-DW-7834 
       44.84        26.27        20.12        11.28        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR 
       12.13        29.26        19.73        17.75        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 
       21.60        15.91        15.62         6.74         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       59.01       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        71.80        62.93 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       40.83        26.04        30.28        25.35         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 
       19.00        24.89        10.68         2.40         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 
       20.52        25.84        25.25        17.98        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.18              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            67.17            194.79 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            20.55             25.35 
[1] "1.2 - 67.2 (20.5)"  "0.1 - 194.8 (25.4)"
[1] "hr=" "3.6"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         6        2         2        3
  8P LOSS WILD-TYPE     165       19        50       12
D53V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 6               165
  STAGE II                2                19
  STAGE III               2                50
  STAGE IV                3                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
  8P LOSS MUTATED     8   3     5
  8P LOSS WILD-TYPE 183  30    57
D53V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                  8               183
  T2                  3                30
  T3+T4               5                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"
                   vv
clus                N0 N1 N2
  8P LOSS MUTATED    1  5  0
  8P LOSS WILD-TYPE 48 19  4
D53V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0               1                48
  N1               5                19
  N2               0                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4  3
  8P LOSS WILD-TYPE 90  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    3
  8P LOSS WILD-TYPE   90    6
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               4                90
  1               3                 6
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     7   9
  8P LOSS WILD-TYPE  69 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7    9
  8P LOSS WILD-TYPE   69  203
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               7                69
  MALE                 9               203
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
D53V10, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                52 
       TCGA-2Z-A9JD        TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     2
  8P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           2    12
  8P LOSS WILD-TYPE                        59   192
D53V11, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      2                59
  WHITE                                         12               192
[1] 4 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
  8P LOSS MUTATED     0  16
  8P LOSS WILD-TYPE  12 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   16
  8P LOSS WILD-TYPE   12  224
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              16               224
[1] 2 2
[1] FALSE

Clustering(54) Variable = 8Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     7   2
  8Q LOSS WILD-TYPE 234  42
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               276 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                42 
$`8Q LOSS MUTATED`
TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-5P-A9K8 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5889 
       67.17        12.99        43.04        37.51        29.03        10.82 
TCGA-F9-A7Q0 TCGA-G7-A8LC TCGA-UN-AAZ9 
       13.08        23.08        18.02 

$`8Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       22.49        12.26        61.05        21.37         0.89        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
       36.49        20.25        16.77        20.32        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        30.28        25.35         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       24.89        10.68         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       20.52        25.84        25.25        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            10.82              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            67.17            194.79 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           23.080            25.315 
[1] "10.8 - 67.2 (23.1)" "0.1 - 194.8 (25.3)"
[1] "hr=" "1.9"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         4        1         1        1
  8Q LOSS WILD-TYPE     167       20        51       14
D54V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 4               167
  STAGE II                1                20
  STAGE III               1                51
  STAGE IV                1                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     6   1     2
  8Q LOSS WILD-TYPE 185  32    60
D54V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1                  6               185
  T2                  1                32
  T3+T4               2                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                N0 N1 N2
  8Q LOSS MUTATED    1  2  0
  8Q LOSS WILD-TYPE 48 22  4
D54V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               1                48
  N1               2                22
  N2               0                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  1
  8Q LOSS WILD-TYPE 92  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    1
  8Q LOSS WILD-TYPE   92    8
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               2                92
  1               1                 8
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     5   4
  8Q LOSS WILD-TYPE  71 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    4
  8Q LOSS WILD-TYPE   71  208
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               5                71
  MALE                 4               208
[1] 2 2
[1] FALSE
D54V8, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                74 
       TCGA-2Z-A9JL        TCGA-2Z-A9JT        TCGA-5P-A9JU        TCGA-DW-5560 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-2Z-A9JE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JK        TCGA-2Z-A9JN        TCGA-4A-A93W        TCGA-4A-A93X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-J7-8537        TCGA-P4-AAVK        TCGA-Q2-A5QZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PL        TCGA-V9-A7HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D54V9, continuous
D54V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2     6
  8Q LOSS WILD-TYPE                        59   198
D54V11, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      2                59
  WHITE                                          6               198
[1] 4 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
  8Q LOSS MUTATED     0   9
  8Q LOSS WILD-TYPE  12 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    9
  8Q LOSS WILD-TYPE   12  231
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               9               231
[1] 2 2
[1] FALSE

Clustering(55) Variable = 9P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    19  14
  9P LOSS WILD-TYPE 222  30
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               33               252 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               14                30 
$`9P LOSS MUTATED`
TCGA-2Z-A9JJ TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-BQ-5888 TCGA-BQ-7056 TCGA-2Z-A9JG 
       39.88        12.99        49.25        13.25        20.12        54.64 
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A57E 
       51.52        12.82        19.36        18.21        19.63         8.48 
TCGA-AL-3466 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A69E TCGA-BQ-5879 TCGA-BQ-5889 
        9.63        29.03        20.61        14.86        22.92        10.82 
TCGA-BQ-7048 TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 
       93.34        79.86        13.08         4.01        11.05        71.44 
TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-HE-7130 TCGA-IA-A40Y TCGA-J7-8537 
       20.52        23.08        16.90        58.19         2.04        10.55 
TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       18.02        86.27        18.64 

$`9P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       12.26        67.17        61.05        21.37         0.89        76.64 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       19.23        26.04        11.97        96.92        44.84        26.27 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       12.39        27.09        67.43         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       14.33        12.46        16.96        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       17.23         0.16        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        30.28        25.35         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        2.76       123.62        48.26        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 
        7.63         7.04         7.17         3.81        40.77        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        2.40         1.18         0.43        51.78        90.90        39.25 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 
       25.15        25.84        25.25        17.98        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 
       96.69        22.26        21.34        12.36        12.76        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       39.06        18.64        18.05        25.28         6.02        13.28 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             2.04              0.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            93.34            194.79 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           19.360            26.025 
[1] "2.0 - 93.3 (19.4)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "4.4"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         9        0        15        6
  9P LOSS WILD-TYPE     162       21        37        9
D55V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 9               162
  STAGE II                0                21
  STAGE III              15                37
  STAGE IV                6                 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
  9P LOSS MUTATED    10   3    20
  9P LOSS WILD-TYPE 181  30    42
D55V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                 10               181
  T2                  3                30
  T3+T4              20                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  9P LOSS MUTATED    6 10  3
  9P LOSS WILD-TYPE 43 14  1
D55V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               6                43
  N1              10                14
  N2               3                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    9  3
  9P LOSS WILD-TYPE 85  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      9    3
  9P LOSS WILD-TYPE   85    6
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               9                85
  1               3                 6
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    17  16
  9P LOSS WILD-TYPE  59 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     17   16
  9P LOSS WILD-TYPE   59  196
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              17                59
  MALE                16               196
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
D55V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     2
  9P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           4    26
  9P LOSS WILD-TYPE                        57   178
D55V11, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      4                57
  WHITE                                         26               178
[1] 4 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
  9P LOSS MUTATED     0  29
  9P LOSS WILD-TYPE  12 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   29
  9P LOSS WILD-TYPE   12  211
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              29               211
[1] 2 2
[1] FALSE

Clustering(56) Variable = 9Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    22  12
  9Q LOSS WILD-TYPE 219  32
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               34               251 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12                32 
$`9Q LOSS MUTATED`
TCGA-2Z-A9JJ TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5888 TCGA-BQ-7055 
       39.88        12.99        49.25        11.87        13.25        26.27 
TCGA-BQ-7056 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-7286 
       20.12        54.64        51.52        12.82        19.36        18.21 
TCGA-A4-7287 TCGA-AL-3466 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-A69E TCGA-BQ-5879 
       19.63         9.63        29.03        34.49        14.86        22.92 
TCGA-BQ-5889 TCGA-BQ-7048 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 
       10.82        93.34        79.86        10.68        13.08         4.01 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LC TCGA-HE-7130 TCGA-IA-A40Y 
       11.05        71.44        20.52        23.08        58.19         2.04 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-UN-AAZ9 TCGA-Y8-A896 
       10.55        10.09        18.02        18.64 

$`9Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       12.26        67.17        61.05        21.37         0.89        76.64 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 
       21.67        27.68        21.07        10.16        21.86        19.23 
TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7058 TCGA-DW-5560 
       26.04        11.97        96.92        44.84        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM 
       56.91         4.57        91.73        56.81        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       67.43         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       33.83        30.58        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        25.35         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
      123.62        48.26        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       74.60        34.19        19.00        24.89         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
        0.43        51.78        90.90        39.25        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE 
       22.26        21.34        12.36        12.76        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             2.04              0.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            93.34            194.79 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            19.00             26.01 
[1] "2.0 - 93.3 (19.0)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "3.8"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED        11        1        15        5
  9Q LOSS WILD-TYPE     160       20        37       10
D56V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                11               160
  STAGE II                1                20
  STAGE III              15                37
  STAGE IV                5                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
  9Q LOSS MUTATED    12   1    21
  9Q LOSS WILD-TYPE 179  32    41
D56V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                 12               179
  T2                  1                32
  T3+T4              21                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                N0 N1 N2
  9Q LOSS MUTATED    6  8  3
  9Q LOSS WILD-TYPE 43 16  1
D56V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0               6                43
  N1               8                16
  N2               3                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   12  2
  9Q LOSS WILD-TYPE 82  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     12    2
  9Q LOSS WILD-TYPE   82    7
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              12                82
  1               2                 7
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    17  17
  9Q LOSS WILD-TYPE  59 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     17   17
  9Q LOSS WILD-TYPE   59  195
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              17                59
  MALE                17               195
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     3
  9Q LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           4    26
  9Q LOSS WILD-TYPE                        57   178
D56V11, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                      4                57
  WHITE                                         26               178
[1] 4 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
  9Q LOSS MUTATED     0  28
  9Q LOSS WILD-TYPE  12 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0   28
  9Q LOSS WILD-TYPE   12  212
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              28               212
[1] 2 2
[1] FALSE

Clustering(57) Variable = 10P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    11   6
  10P LOSS WILD-TYPE 230  38
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                268 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 38 
$`10P LOSS MUTATED`
TCGA-5P-A9JU TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-2Z-A9J8 TCGA-5P-A9KH 
       12.26        12.99        49.25        11.87        91.73        67.43 
TCGA-AL-3466 TCGA-B9-4116 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-DZ-6131 TCGA-G7-6789 
        9.63        20.61        19.27        21.63        79.86         4.01 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-Q2-A5QZ 
       20.52        25.84        23.08         3.68        14.07 

$`10P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       22.49        67.17        61.05        21.37         0.89        76.64 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 
       21.67        27.68        21.07        10.16        21.86        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 
       21.60        15.91        15.62         6.74         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE 
       59.01        58.22       100.27        56.91         4.57        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        26.40         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
        3.81        40.77        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.15        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              3.68               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             91.73             194.79 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            20.520             25.825 
[1] "3.7 - 91.7 (20.5)"  "0.1 - 194.8 (25.8)"
[1] "hr=" "3.1"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         4        0         9        2
  10P LOSS WILD-TYPE     167       21        43       13
D57V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  4                167
  STAGE II                 0                 21
  STAGE III                9                 43
  STAGE IV                 2                 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
  10P LOSS MUTATED     6   1    10
  10P LOSS WILD-TYPE 185  32    52
D57V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                   6                185
  T2                   1                 32
  T3+T4               10                 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"
                    vv
clus                 N0 N1 N2
  10P LOSS MUTATED    3  4  1
  10P LOSS WILD-TYPE 46 20  3
D57V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                3                 46
  N1                4                 20
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    3  1
  10P LOSS WILD-TYPE 91  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3    1
  10P LOSS WILD-TYPE   91    8
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                3                 91
  1                1                  8
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6  11
  10P LOSS WILD-TYPE  70 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6   11
  10P LOSS WILD-TYPE   70  201
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                6                 70
  MALE                 11                201
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
D57V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     0
  10P LOSS WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           4    12
  10P LOSS WILD-TYPE                        57   192
D57V11, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       4                 57
  WHITE                                          12                192
[1] 4 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
  10P LOSS MUTATED     0  14
  10P LOSS WILD-TYPE  12 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0   14
  10P LOSS WILD-TYPE   12  226
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               14                226
[1] 2 2
[1] FALSE

Clustering(58) Variable = 10Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    10   8
  10Q LOSS WILD-TYPE 231  36
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                18                267 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                 36 
$`10Q LOSS MUTATED`
TCGA-5P-A9JU TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-2Z-A9J8 TCGA-5P-A9KH 
       12.26        12.99        49.25        11.87        91.73        67.43 
TCGA-AL-3466 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 
        9.63        19.27        21.63        79.86         4.01        20.52 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
       25.84        23.08         3.68        10.55        14.07        86.27 

$`10Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       22.49        67.17        61.05        21.37         0.89        76.64 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 
       21.67        27.68        21.07        10.16        21.86        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 
       21.60        15.91        15.62         6.74         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE 
       59.01        58.22       100.27        56.91         4.57        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       47.80        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        7.17         3.81        40.77        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       71.44        25.15        25.25        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
      194.79        12.92        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              3.68               0.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             91.73             194.79 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            19.895             25.640 
[1] "3.7 - 91.7 (19.9)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "3.7"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         4        0        11        2
  10Q LOSS WILD-TYPE     167       21        41       13
D58V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  4                167
  STAGE II                 0                 21
  STAGE III               11                 41
  STAGE IV                 2                 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
  10Q LOSS MUTATED     6   1    11
  10Q LOSS WILD-TYPE 185  32    51
D58V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                   6                185
  T2                   1                 32
  T3+T4               11                 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                 N0 N1 N2
  10Q LOSS MUTATED    3  6  1
  10Q LOSS WILD-TYPE 46 18  3
D58V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                3                 46
  N1                6                 18
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    4  1
  10Q LOSS WILD-TYPE 90  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4    1
  10Q LOSS WILD-TYPE   90    8
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                4                 90
  1                1                  8
[1] 2 2
[1] FALSE
D58V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6  12
  10Q LOSS WILD-TYPE  70 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   12
  10Q LOSS WILD-TYPE   70  200
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                6                 70
  MALE                 12                200
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     1
  10Q LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           4    12
  10Q LOSS WILD-TYPE                        57   192
D58V11, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       4                 57
  WHITE                                          12                192
[1] 4 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
  10Q LOSS MUTATED     0  15
  10Q LOSS WILD-TYPE  12 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0   15
  10Q LOSS WILD-TYPE   12  225
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               15                225
[1] 2 2
[1] FALSE

Clustering(59) Variable = 11P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    11   6
  11P LOSS WILD-TYPE 230  38
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                17                268 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 38 
$`11P LOSS MUTATED`
TCGA-2Z-A9JG TCGA-4A-A93X TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-A4-7287 TCGA-B1-7332 
       54.64        12.82        43.04        19.36        19.63        37.51 
TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-G7-6789 TCGA-G7-7502 
       34.49        19.27         8.88        21.63         4.01        25.84 
TCGA-G7-A8LD TCGA-HE-7130 TCGA-IA-A40Y TCGA-Y8-A896 TCGA-Y8-A8S1 
       16.90        58.19         2.04        18.64        13.28 

$`11P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI 
      100.27        56.91         4.57        91.73        56.81        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        71.80        62.93        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        18.21         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
       62.66        67.73         2.20        41.13        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 
       16.77        20.32        33.83        29.03        30.58        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       12.30        86.76        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       71.44        25.15        20.52        25.25        17.98        23.08 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        18.05        25.28         6.02 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              2.04               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             58.19             194.79 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             19.36              25.61 
[1] "2.0 - 58.2 (19.4)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "4"  
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         5        2         5        3
  11P LOSS WILD-TYPE     166       19        47       12
D59V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  5                166
  STAGE II                 2                 19
  STAGE III                5                 47
  STAGE IV                 3                 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     5   2    10
  11P LOSS WILD-TYPE 186  31    52
D59V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   5                186
  T2                   2                 31
  T3+T4               10                 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"
                    vv
clus                 N0 N1 N2
  11P LOSS MUTATED    1  4  2
  11P LOSS WILD-TYPE 48 20  2
D59V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                1                 48
  N1                4                 20
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    4  1
  11P LOSS WILD-TYPE 90  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    1
  11P LOSS WILD-TYPE   90    8
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                4                 90
  1                1                  8
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     7  10
  11P LOSS WILD-TYPE  69 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      7   10
  11P LOSS WILD-TYPE   69  202
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                7                 69
  MALE                 10                202
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 72 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         TCGA-2Z-A9JN 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-5P-A9K3         TCGA-5P-A9KE         TCGA-A4-8310 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4114         TCGA-B9-4115 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-7268         TCGA-B9-A69E 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6792 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LE         TCGA-GL-7773 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IA-A83V         TCGA-MH-A854         TCGA-MH-A856 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-Q2-A5QZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A8RY 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D59V10, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 52 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6793         TCGA-G7-6795 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-Y8-A8RY 
"11P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           2    13
  11P LOSS WILD-TYPE                        59   191
D59V11, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       2                 59
  WHITE                                          13                191
[1] 4 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
  11P LOSS MUTATED     0  13
  11P LOSS WILD-TYPE  12 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   13
  11P LOSS WILD-TYPE   12  227
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               13                227
[1] 2 2
[1] FALSE

Clustering(60) Variable = 11Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    13   8
  11Q LOSS WILD-TYPE 228  36
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                264 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 36 
$`11Q LOSS MUTATED`
TCGA-B9-A44B TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K9 TCGA-B1-7332 
       11.87        54.64        51.52        12.82        19.36        37.51 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-7044 
       19.27         8.88        21.63        10.82         7.66       123.62 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-HE-7130 TCGA-IA-A40Y 
        0.43         4.01        11.05        25.84        58.19         2.04 
TCGA-J7-8537 TCGA-UZ-A9PQ TCGA-Y8-A896 
       10.55        86.27        18.64 

$`11Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       10.16        21.86        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM 
       56.91         4.57        91.73        56.81        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
       62.66        67.73         2.20        41.13        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       17.49        12.30        86.76        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5891 
       47.80        40.83        26.04        30.28        25.35         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        7.92         2.76        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
       24.89        10.68        13.08         2.40         1.18        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       90.90        39.25        71.44        25.15        20.52        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       39.06        18.64        18.05        25.28         6.02        13.28 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.43               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            123.62             194.79 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            18.640             25.825 
[1] "0.4 - 123.6 (18.6)" "0.1 - 194.8 (25.8)"
[1] "hr=" "3.5"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         3        1        11        5
  11Q LOSS WILD-TYPE     168       20        41       10
D60V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  3                168
  STAGE II                 1                 20
  STAGE III               11                 41
  STAGE IV                 5                 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
  11Q LOSS MUTATED     3   2    16
  11Q LOSS WILD-TYPE 188  31    46
D60V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   3                188
  T2                   2                 31
  T3+T4               16                 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"
                    vv
clus                 N0 N1 N2
  11Q LOSS MUTATED    3  6  3
  11Q LOSS WILD-TYPE 46 18  1
D60V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                3                 46
  N1                6                 18
  N2                3                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    7  2
  11Q LOSS WILD-TYPE 87  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      7    2
  11Q LOSS WILD-TYPE   87    7
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                7                 87
  1                2                  7
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     7  14
  11Q LOSS WILD-TYPE  69 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      7   14
  11Q LOSS WILD-TYPE   69  198
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                7                 69
  MALE                 14                198
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           4    13
  11Q LOSS WILD-TYPE                        57   191
D60V11, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       4                 57
  WHITE                                          13                191
[1] 4 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
  11Q LOSS MUTATED     0  16
  11Q LOSS WILD-TYPE  12 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   16
  11Q LOSS WILD-TYPE   12  224
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               16                224
[1] 2 2
[1] FALSE

Clustering(61) Variable = 13Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    14  10
  13Q LOSS WILD-TYPE 227  34
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                24                261 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                 34 
$`13Q LOSS MUTATED`
TCGA-AL-A5DJ TCGA-B3-A6W5 TCGA-2Z-A9JI TCGA-5P-A9K8 TCGA-A4-7287 TCGA-A4-7915 
       49.25        10.16        51.52        43.04        19.63         0.23 
TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-F9-A4JJ 
       29.03        86.76        22.92        21.63         2.76        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD 
       13.08         4.01        11.05        25.84        23.08        16.90 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 
        3.68         2.04        10.55        42.94        14.07        18.02 

$`13Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B9-5155 
       12.99        76.64        21.67        27.68        21.07        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JM 
        4.57        91.73        56.81        54.64        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        18.21         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        7.82        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       16.77        20.32        33.83        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       12.30        19.27         8.88        63.72        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        0.95         7.92       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       19.00        24.89         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       90.90        39.25        71.44        25.15        20.52        25.25 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       17.98        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB 
       31.13        15.48        99.78        87.09         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.23               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             86.76             194.79 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             17.46              26.01 
[1] "0.2 - 86.8 (17.5)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "5.6"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         7        1        12        3
  13Q LOSS WILD-TYPE     164       20        40       12
D61V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  7                164
  STAGE II                 1                 20
  STAGE III               12                 40
  STAGE IV                 3                 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
  13Q LOSS MUTATED     7   2    15
  13Q LOSS WILD-TYPE 184  31    47
D61V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                   7                184
  T2                   2                 31
  T3+T4               15                 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"
                    vv
clus                 N0 N1 N2
  13Q LOSS MUTATED    3  7  2
  13Q LOSS WILD-TYPE 46 17  2
D61V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                3                 46
  N1                7                 17
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    7  1
  13Q LOSS WILD-TYPE 87  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      7    1
  13Q LOSS WILD-TYPE   87    8
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                7                 87
  1                1                  8
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    16   8
  13Q LOSS WILD-TYPE  60 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     16    8
  13Q LOSS WILD-TYPE   60  204
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               16                 60
  MALE                  8                204
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
D61V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     2
  13Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           5    15
  13Q LOSS WILD-TYPE                        56   189
D61V11, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       5                 56
  WHITE                                          15                189
[1] 4 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
  13Q LOSS MUTATED     1  19
  13Q LOSS WILD-TYPE  11 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   19
  13Q LOSS WILD-TYPE   11  221
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               19                221
[1] 2 2
[1] FALSE

Clustering(62) Variable = 14Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    33  14
  14Q LOSS WILD-TYPE 208  30
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                47                238 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                14                 30 
$`14Q LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-BQ-5888 TCGA-PJ-A5Z8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       12.99        49.25        13.25        19.73        54.64        51.52 
TCGA-2Z-A9JK TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-7287 
       38.99        15.48        43.04        19.36        18.21        19.63 
TCGA-A4-7583 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 
        0.10        29.46         9.63        62.66        67.73        37.51 
TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5885 
       16.77        29.03        20.61        17.23        19.27        30.28 
TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       10.82         2.76        79.86        80.88        10.68        13.08 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
        4.01        11.05        71.44        20.52        25.84        23.08 
TCGA-G7-A8LD TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40Y TCGA-MH-A854 
       16.90        27.65        73.25        16.80         2.04        17.62 
TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-WN-A9G9 
        6.61        14.07        18.02        37.35        26.01 

$`14Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       11.87        19.23        26.04        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       12.13        29.26        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 
       21.60        15.91        15.62         6.74         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       56.81        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC 
       22.26        78.64        71.80        62.93        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       27.09        67.43        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
        8.48        16.31        15.75         8.28        12.46        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
       49.32        66.71         2.20        41.13        36.49        20.25 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40         0.46         1.15        43.99        22.06 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 
        0.16        14.86        17.49        12.30        86.76         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 
       26.04        25.35         7.66         0.95         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6135 
        7.04         7.17         3.81        40.77        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       34.19        19.00        24.89         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB 
       51.78        90.90        39.25        25.15        25.25        17.98 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92         3.68         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       11.84        56.75        25.22        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       30.38        27.65        20.25        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.09        42.94        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        51.35        31.73        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.10               0.13 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             80.88             194.79 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            19.630             26.025 
[1] "0.1 - 80.9 (19.6)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "3.4"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        18        3        14        6
  14Q LOSS WILD-TYPE     153       18        38        9
D62V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 18                153
  STAGE II                 3                 18
  STAGE III               14                 38
  STAGE IV                 6                  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
  14Q LOSS MUTATED    20   5    22
  14Q LOSS WILD-TYPE 171  28    40
D62V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                  20                171
  T2                   5                 28
  T3+T4               22                 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                 N0 N1 N2
  14Q LOSS MUTATED    8  8  4
  14Q LOSS WILD-TYPE 41 16  0
D62V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                8                 41
  N1                8                 16
  N2                4                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   12  3
  14Q LOSS WILD-TYPE 82  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12    3
  14Q LOSS WILD-TYPE   82    6
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               12                 82
  1                3                  6
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    21  26
  14Q LOSS WILD-TYPE  55 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     21   26
  14Q LOSS WILD-TYPE   55  186
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               21                 55
  MALE                 26                186
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     1
  14Q LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          10    33
  14Q LOSS WILD-TYPE                        51   171
D62V11, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                      10                 51
  WHITE                                          33                171
[1] 4 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
  14Q LOSS MUTATED     1  40
  14Q LOSS WILD-TYPE  11 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   40
  14Q LOSS WILD-TYPE   11  200
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               40                200
[1] 2 2
[1] FALSE

Clustering(63) Variable = 15Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    22   9
  15Q LOSS WILD-TYPE 219  35
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                31                254 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 9                 35 
$`15Q LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-PJ-A5Z8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9JY 
       12.99        19.73        54.64        51.52        12.82        49.58 
TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-A5W8 
       19.36        18.21         0.10        41.13        29.03        17.23 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       22.92        21.63        10.82         2.76        10.68        13.08 
TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 
        4.01        71.44        25.84        23.08       194.79         3.68 
TCGA-HE-7130 TCGA-HE-A5NK TCGA-P4-A5EA TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-Y8-A896 
       58.19        73.25         6.61        18.02        98.96        18.64 
TCGA-Y8-A8S1 
       13.28 

$`15Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       67.17        16.34        12.13        29.26        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
        4.57        91.73        56.81        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 
       43.04        12.99        12.39        27.09        67.43        19.63 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 
       49.32        66.71        62.66        67.73         2.20        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
       36.49        20.25        16.77        20.32        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E 
        0.46         1.15        43.99        22.06         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         0.95         7.92       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       34.19        19.00        24.89         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 
       51.78        90.90        11.05        39.25        25.15        20.52 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 
       25.25        17.98        16.90        80.65        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       26.01        11.84        56.75        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 
       51.35        31.73        26.01        39.06        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.10               0.13 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            194.79             129.86 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             19.36              26.01 
[1] "0.1 - 194.8 (19.4)" "0.1 - 129.9 (26.0)"
[1] "hr=" "2.4"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED        11        1        10        5
  15Q LOSS WILD-TYPE     160       20        42       10
D63V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                 11                160
  STAGE II                 1                 20
  STAGE III               10                 42
  STAGE IV                 5                 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
  15Q LOSS MUTATED    13   2    16
  15Q LOSS WILD-TYPE 178  31    46
D63V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                  13                178
  T2                   2                 31
  T3+T4               16                 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"
                    vv
clus                 N0 N1 N2
  15Q LOSS MUTATED    4  8  2
  15Q LOSS WILD-TYPE 45 16  2
D63V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                4                 45
  N1                8                 16
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   10  2
  15Q LOSS WILD-TYPE 84  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     10    2
  15Q LOSS WILD-TYPE   84    7
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               10                 84
  1                2                  7
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    11  20
  15Q LOSS WILD-TYPE  65 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     11   20
  15Q LOSS WILD-TYPE   65  192
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               11                 65
  MALE                 20                192
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
D63V10, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 52 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JN         TCGA-2Z-A9JO         TCGA-4A-A93W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-A48D         TCGA-A4-A57E 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3472         TCGA-AL-7173 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4114         TCGA-B9-4117 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-7963         TCGA-F9-A97G 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RY 
"15Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     1
  15Q LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           4    22
  15Q LOSS WILD-TYPE                        57   182
D63V11, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       4                 57
  WHITE                                          22                182
[1] 4 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
  15Q LOSS MUTATED     1  25
  15Q LOSS WILD-TYPE  11 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   25
  15Q LOSS WILD-TYPE   11  215
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               25                215
[1] 2 2
[1] FALSE

Clustering(64) Variable = 16P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     1   3
  16P LOSS WILD-TYPE 240  41
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                281 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 41 
$`16P LOSS MUTATED`
TCGA-A4-7287 TCGA-BQ-5882 TCGA-G7-6793 TCGA-HE-7130 
       19.63        21.63        11.05        58.19 

$`16P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.62         6.74         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       18.21         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       90.90        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             11.05               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             58.19             194.79 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             20.63              25.35 
[1] "11.1 - 58.2 (20.6)" "0.1 - 194.8 (25.4)"
[1] "hr=" "6.4"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         1        0         2        1
  16P LOSS WILD-TYPE     170       21        50       14
D64V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                170
  STAGE II                 0                 21
  STAGE III                2                 50
  STAGE IV                 1                 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
  16P LOSS MUTATED     1   0     3
  16P LOSS WILD-TYPE 190  33    59
D64V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   1                190
  T2                   0                 33
  T3+T4                3                 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                 N0 N1 N2
  16P LOSS MUTATED    1  0  1
  16P LOSS WILD-TYPE 48 24  3
D64V5, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 75 
        TCGA-5P-A9JU         TCGA-A4-A5Y1         TCGA-B1-A47O 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A657         TCGA-BQ-5888         TCGA-BQ-5892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-IA-A83W         TCGA-Y8-A8RZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J1         TCGA-2Z-A9JO         TCGA-4A-A93W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-4A-A93X         TCGA-4A-A93Y         TCGA-5P-A9K9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A7UZ         TCGA-AL-3466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-A655         TCGA-B1-A656 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5885 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5889         TCGA-BQ-5890 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5893         TCGA-BQ-5894 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-DW-7963         TCGA-DZ-6131 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-G7-A8LD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-GL-A59R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A9DC         TCGA-IA-A40U         TCGA-IA-A40Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-J7-A8I2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KV-A74V         TCGA-P4-A5E6         TCGA-P4-A5E8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-P4-AAVK         TCGA-P4-AAVL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A7SM         TCGA-SX-A7SP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UN-AAZ9         TCGA-UZ-A9PM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PQ         TCGA-UZ-A9PX         TCGA-Y8-A897 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D64V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  0
  16P LOSS WILD-TYPE 92  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    0
  16P LOSS WILD-TYPE   92    9
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                2                 92
  1                0                  9
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3   1
  16P LOSS WILD-TYPE  73 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    1
  16P LOSS WILD-TYPE   73  211
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 73
  MALE                  1                211
[1] 2 2
[1] FALSE
D64V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 75 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8098 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-7963         TCGA-EV-5901 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-F9-A7Q0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-P4-AAVK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SU         TCGA-UZ-A9PL         TCGA-V9-A7HT 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D64V9, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 73 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         TCGA-2Z-A9JN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-5P-A9K3         TCGA-5P-A9KE         TCGA-A4-8310 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4114         TCGA-B9-4115 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-7268         TCGA-B9-A69E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6792 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-G7-A8LB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A83V         TCGA-MH-A854         TCGA-MH-A856 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-Q2-A5QZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A8RY 
"16P LOSS WILD-TYPE" 
D64V10, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 53 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6795         TCGA-G7-7501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           0     2
  16P LOSS WILD-TYPE                        61   202
D64V11, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                271 
        TCGA-2Z-A9J9         TCGA-2Z-A9JD         TCGA-2Z-A9JJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JL         TCGA-2Z-A9JQ         TCGA-2Z-A9JS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JT         TCGA-5P-A9JU         TCGA-5P-A9JV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7288         TCGA-A4-7584         TCGA-A4-7734 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5Y1         TCGA-AL-3468         TCGA-AL-A5DJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A47M         TCGA-B1-A47O         TCGA-B1-A657 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-A6W5         TCGA-B9-5155         TCGA-B9-A44B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A5W7         TCGA-BQ-5886         TCGA-BQ-5888 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-7046         TCGA-BQ-7049 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6134         TCGA-GL-A59T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A83W         TCGA-IZ-A6M8         TCGA-MH-A855 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A857         TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PZ         TCGA-Y8-A895         TCGA-Y8-A898 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-2K-A9WE         TCGA-2Z-A9J1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J2         TCGA-2Z-A9J3         TCGA-2Z-A9J5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J6         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JG         TCGA-2Z-A9JI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         TCGA-2Z-A9JN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-2Z-A9JP         TCGA-2Z-A9JR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-5P-A9JW         TCGA-5P-A9JY         TCGA-5P-A9JZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-5P-A9K0         TCGA-5P-A9K2         TCGA-5P-A9K3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-5P-A9K4         TCGA-5P-A9K6         TCGA-5P-A9K8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-5P-A9K9         TCGA-5P-A9KA         TCGA-5P-A9KC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-5P-A9KE         TCGA-5P-A9KH         TCGA-A4-7286 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7828         TCGA-A4-7915         TCGA-A4-7996 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7997         TCGA-A4-8098         TCGA-A4-8310 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8515 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8516         TCGA-A4-8517         TCGA-A4-8518 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A48D         TCGA-A4-A4ZT 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5DU         TCGA-A4-A5XZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-A4-A6HP         TCGA-A4-A772 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A7UZ         TCGA-AL-3466         TCGA-AL-3467 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-AT-A5NU         TCGA-B1-5398 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B1-A47N         TCGA-B1-A654 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B3-3925 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5156         TCGA-B9-7268 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A5W8         TCGA-B9-A5W9         TCGA-B9-A69E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A8YH         TCGA-B9-A8YI         TCGA-BQ-5875 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5889         TCGA-BQ-5890 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5893         TCGA-BQ-7044 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7059 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-DZ-6131         TCGA-DZ-6133 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F9-A4JJ         TCGA-F9-A7Q0         TCGA-F9-A7VF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6795 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-G7-A4TM         TCGA-G7-A8LB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LC         TCGA-G7-A8LD         TCGA-G7-A8LE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7773         TCGA-GL-7966 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A9DC         TCGA-GL-A9DD         TCGA-GL-A9DE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IA-A83T         TCGA-IA-A83V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196         TCGA-IZ-A6M9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-J7-A8I2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KV-A6GD         TCGA-KV-A6GE         TCGA-KV-A74V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A55W         TCGA-MH-A55Z         TCGA-MH-A560 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A561         TCGA-MH-A562         TCGA-MH-A854 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-O9-A75Z         TCGA-P4-A5E6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5E8         TCGA-P4-A5EA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-P4-A5ED         TCGA-P4-AAVK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-AAVL         TCGA-P4-AAVM         TCGA-P4-AAVO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UN-AAZ9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PJ         TCGA-UZ-A9PK         TCGA-UZ-A9PL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PN         TCGA-UZ-A9PP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PQ         TCGA-UZ-A9PS         TCGA-UZ-A9PU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PV         TCGA-UZ-A9PX         TCGA-UZ-A9Q0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9Q1         TCGA-V9-A7HT         TCGA-WN-A9G9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A897         TCGA-Y8-A8RY         TCGA-Y8-A8S0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A8S1 
"16P LOSS WILD-TYPE" 
D64V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   2
  16P LOSS WILD-TYPE  12 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    2
  16P LOSS WILD-TYPE   12  238
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                2                238
[1] 2 2
[1] FALSE

Clustering(65) Variable = 16Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     2   5
  16Q LOSS WILD-TYPE 239  39
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                278 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 39 
$`16Q LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-2Z-A9JI TCGA-A4-7287 TCGA-BQ-5882 TCGA-G7-6793 TCGA-G7-A8LD 
       12.99        51.52        19.63        21.63        11.05        16.90 
TCGA-HE-7130 
       58.19 

$`16Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK 
       56.91         4.57        91.73        56.81        54.64        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 
       12.99        12.39        27.09        67.43        18.21         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        1.18         0.43         4.01        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       23.08        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             11.05               0.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             58.19             194.79 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            19.630             25.465 
[1] "11.1 - 58.2 (19.6)" "0.1 - 194.8 (25.5)"
[1] "hr=" "6.2"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         1        0         5        1
  16Q LOSS WILD-TYPE     170       21        47       14
D65V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                170
  STAGE II                 0                 21
  STAGE III                5                 47
  STAGE IV                 1                 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
  16Q LOSS MUTATED     2   0     5
  16Q LOSS WILD-TYPE 189  33    57
D65V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   2                189
  T2                   0                 33
  T3+T4                5                 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"
                    vv
clus                 N0 N1 N2
  16Q LOSS MUTATED    1  2  1
  16Q LOSS WILD-TYPE 48 22  3
D65V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                1                 48
  N1                2                 22
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  0
  16Q LOSS WILD-TYPE 92  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    0
  16Q LOSS WILD-TYPE   92    9
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                2                 92
  1                0                  9
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3   4
  16Q LOSS WILD-TYPE  73 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    4
  16Q LOSS WILD-TYPE   73  208
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 73
  MALE                  4                208
[1] 2 2
[1] FALSE
D65V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 74 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8098 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-7963         TCGA-EV-5901 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-F9-A7Q0 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-J7-8537         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-SX-A7SU 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PL         TCGA-V9-A7HT 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D65V9, continuous
D65V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           0     5
  16Q LOSS WILD-TYPE                        61   199
D65V11, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 61
  WHITE                                           5                199
[1] 4 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
  16Q LOSS MUTATED     0   5
  16Q LOSS WILD-TYPE  12 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    5
  16Q LOSS WILD-TYPE   12  235
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                5                235
[1] 2 2
[1] FALSE

Clustering(66) Variable = 17P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     6   7
  17P LOSS WILD-TYPE 235  37
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                272 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                 37 
$`17P LOSS MUTATED`
TCGA-BQ-7058 TCGA-2Z-A9JI TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-5P-A9KH TCGA-A4-7287 
       11.28        51.52        15.48        19.36        67.43        19.63 
TCGA-A4-7915 TCGA-A4-A57E TCGA-AL-3466 TCGA-G7-6793 TCGA-HE-7130 TCGA-J7-A8I2 
        0.23         8.48         9.63        11.05        58.19        10.09 
TCGA-Q2-A5QZ 
       14.07 

$`17P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 
       11.97        96.92        44.84        26.27        20.12        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.74         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK 
       56.91         4.57        91.73        56.81        54.64        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       27.09        18.21         0.10        35.18        19.13         7.82 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
       16.96        16.31        15.75         8.28        12.46        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             67.43             194.79 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             14.07              25.74 
[1] "0.2 - 67.4 (14.1)"  "0.1 - 194.8 (25.7)"
[1] "hr=" "6.4"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         2        1         4        3
  17P LOSS WILD-TYPE     169       20        48       12
D66V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  2                169
  STAGE II                 1                 20
  STAGE III                4                 48
  STAGE IV                 3                 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
  17P LOSS MUTATED     3   3     7
  17P LOSS WILD-TYPE 188  30    55
D66V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                   3                188
  T2                   3                 30
  T3+T4                7                 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                 N0 N1 N2
  17P LOSS MUTATED    3  1  2
  17P LOSS WILD-TYPE 46 23  2
D66V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                3                 46
  N1                1                 23
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    3  2
  17P LOSS WILD-TYPE 91  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    2
  17P LOSS WILD-TYPE   91    7
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                3                 91
  1                2                  7
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     6   7
  17P LOSS WILD-TYPE  70 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    7
  17P LOSS WILD-TYPE   70  205
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                6                 70
  MALE                  7                205
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
D66V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     1
  17P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           2     9
  17P LOSS WILD-TYPE                        59   195
D66V11, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       2                 59
  WHITE                                           9                195
[1] 4 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
  17P LOSS MUTATED     0  12
  17P LOSS WILD-TYPE  12 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0   12
  17P LOSS WILD-TYPE   12  228
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               12                228
[1] 2 2
[1] FALSE

Clustering(67) Variable = 18P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    27  15
  18P LOSS WILD-TYPE 214  29
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                42                243 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                15                 29 
$`18P LOSS MUTATED`
TCGA-2Z-A9JJ TCGA-AL-A5DJ TCGA-BQ-7058 TCGA-DW-7840 TCGA-SX-A7SO TCGA-2Z-A9JG 
       39.88        49.25        11.28         3.75        41.33        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JP TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9K3 TCGA-5P-A9K9 
       51.52        29.36        12.82       106.55        15.48        19.36 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-8310 TCGA-A4-A57E TCGA-B1-7332 TCGA-B1-A656 
       18.21        19.63        25.64         8.48        37.51        20.32 
TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 
       29.03        20.61         8.88        22.92        21.63        25.35 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7059 TCGA-EV-5903 TCGA-F9-A4JJ 
        2.76       123.62        93.34         7.63        24.89        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-GL-7773 TCGA-GL-7966 TCGA-HE-7130 TCGA-IA-A40Y 
       13.08         4.01        12.92         3.68        58.19         2.04 
TCGA-J7-8537 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-Y8-A8S1 
       10.55         6.61        16.01        14.07        11.93        13.28 

$`18P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       44.84        26.27        20.12        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
       35.93        37.55        24.46        13.78        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       29.26        19.73        17.75        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JR TCGA-4A-A93W 
       38.99        30.71        24.33        31.20         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 
       11.57        49.58        90.21        22.26        78.64        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       30.48        29.46        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
       19.63        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.25        16.77        33.83        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        26.40         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       86.76        19.27        63.72        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        30.28        10.82         7.66         0.95         7.92 
TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7061 
       48.26        61.28        50.40        49.84         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       34.19        19.00         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
      194.79        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94        99.12        92.58        52.27        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN 
       47.90        49.45        44.61        28.80        27.06        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.05        25.28         6.02 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              2.04               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            123.62             194.79 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            18.785             26.200 
[1] "2.0 - 123.6 (18.8)" "0.1 - 194.8 (26.2)"
[1] "hr=" "4.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED        13        1        17        6
  18P LOSS WILD-TYPE     158       20        35        9
D67V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                 13                158
  STAGE II                 1                 20
  STAGE III               17                 35
  STAGE IV                 6                  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
  18P LOSS MUTATED    14   4    24
  18P LOSS WILD-TYPE 177  29    38
D67V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                  14                177
  T2                   4                 29
  T3+T4               24                 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                 N0 N1 N2
  18P LOSS MUTATED    6  9  2
  18P LOSS WILD-TYPE 43 15  2
D67V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                6                 43
  N1                9                 15
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   15  4
  18P LOSS WILD-TYPE 79  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     15    4
  18P LOSS WILD-TYPE   79    5
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               15                 79
  1                4                  5
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    17  25
  18P LOSS WILD-TYPE  59 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     17   25
  18P LOSS WILD-TYPE   59  187
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               17                 59
  MALE                 25                187
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
D67V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     2
  18P LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           7    30
  18P LOSS WILD-TYPE                        54   174
D67V11, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       7                 54
  WHITE                                          30                174
[1] 4 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
  18P LOSS MUTATED     2  33
  18P LOSS WILD-TYPE  10 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   33
  18P LOSS WILD-TYPE   10  207
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               33                207
[1] 2 2
[1] FALSE

Clustering(68) Variable = 18Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    28  16
  18Q LOSS WILD-TYPE 213  28
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                44                241 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                16                 28 
$`18Q LOSS MUTATED`
TCGA-2Z-A9JJ TCGA-A4-A5Y1 TCGA-BQ-7058 TCGA-DW-7840 TCGA-SX-A7SO TCGA-2Z-A9JG 
       39.88        12.99        11.28         3.75        41.33        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JP TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9K3 TCGA-5P-A9K9 
       51.52        29.36        12.82       106.55        15.48        19.36 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-8310 TCGA-A4-A57E TCGA-B1-7332 TCGA-B1-A656 
       18.21        19.63        25.64         8.48        37.51        20.32 
TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 
       29.03        20.61         8.88        22.92        21.63        25.35 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7059 TCGA-EV-5903 TCGA-F9-A4JJ 
        2.76       123.62        93.34         7.63        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 
       13.08         0.43         4.01        16.90        12.92         3.68 
TCGA-HE-7130 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-SX-A7SM 
       58.19         2.04        10.55         6.61        14.07        11.93 
TCGA-UZ-A9PQ TCGA-Y8-A8S1 
       86.27        13.28 

$`18Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       12.26        67.17        61.05        21.37         0.89        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       44.84        26.27        20.12        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
       35.93        37.55        24.46        13.78        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       29.26        19.73        17.75        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       15.91        15.62         6.74         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JR TCGA-4A-A93W 
       38.99        30.71        24.33        31.20         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 
       11.57        49.58        90.21        22.26        78.64        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       30.48        29.46        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
       19.63        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.25        16.77        33.83        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        26.40         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       86.76        19.27        63.72        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        30.28        10.82         7.66         0.95         7.92 
TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7061 
       48.26        61.28        50.40        49.84         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
       34.19        19.00         2.40         1.18        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 
       25.25        17.98        23.08        80.65       194.79        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       31.13        15.48        99.78        87.09        42.94        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       49.45        44.61        28.80        27.06        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 
        6.02 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.43               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            123.62             194.79 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            17.555             26.270 
[1] "0.4 - 123.6 (17.6)" "0.1 - 194.8 (26.3)"
[1] "hr=" "4.4"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED        13        1        19        6
  18Q LOSS WILD-TYPE     158       20        33        9
D68V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 13                158
  STAGE II                 1                 20
  STAGE III               19                 33
  STAGE IV                 6                  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
  18Q LOSS MUTATED    15   5    24
  18Q LOSS WILD-TYPE 176  28    38
D68V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                  15                176
  T2                   5                 28
  T3+T4               24                 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                 N0 N1 N2
  18Q LOSS MUTATED    6 12  2
  18Q LOSS WILD-TYPE 43 12  2
D68V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                6                 43
  N1               12                 12
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   16  4
  18Q LOSS WILD-TYPE 78  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     16    4
  18Q LOSS WILD-TYPE   78    5
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               16                 78
  1                4                  5
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    16  28
  18Q LOSS WILD-TYPE  60 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     16   28
  18Q LOSS WILD-TYPE   60  184
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               16                 60
  MALE                 28                184
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     3
  18Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           8    30
  18Q LOSS WILD-TYPE                        53   174
D68V11, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                       8                 53
  WHITE                                          30                174
[1] 4 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
  18Q LOSS MUTATED     1  36
  18Q LOSS WILD-TYPE  11 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1   36
  18Q LOSS WILD-TYPE   11  204
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               36                204
[1] 2 2
[1] FALSE

Clustering(69) Variable = 19P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    12   4
  19P LOSS WILD-TYPE 229  40
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                269 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 40 
$`19P LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-2Z-A9JG TCGA-5P-A9KC TCGA-A4-7286 TCGA-A4-8310 
       12.99        11.87        54.64        12.39        18.21        25.64 
TCGA-B1-7332 TCGA-BQ-5876 TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD 
       37.51        19.27         0.95         4.01        25.84        16.90 
TCGA-IA-A40Y TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-UZ-A9PN 
        2.04        99.12        14.07        37.35 

$`19P LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       21.86        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
        4.57        91.73        56.81        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 
        7.82         0.23        16.64        30.48        29.46        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       67.73         2.20        41.13        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.82         7.66         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        71.44        25.15        20.52        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       23.08        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       78.90        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.95               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             99.12             194.79 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            17.555             25.580 
[1] "0.9 - 99.1 (17.6)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "2.4"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         4        1         8        1
  19P LOSS WILD-TYPE     167       20        44       14
D69V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  4                167
  STAGE II                 1                 20
  STAGE III                8                 44
  STAGE IV                 1                 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
  19P LOSS MUTATED     6   1     9
  19P LOSS WILD-TYPE 185  32    53
D69V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                   6                185
  T2                   1                 32
  T3+T4                9                 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                 N0 N1 N2
  19P LOSS MUTATED    1  3  1
  19P LOSS WILD-TYPE 48 21  3
D69V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                1                 48
  N1                3                 21
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  0
  19P LOSS WILD-TYPE 92  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    0
  19P LOSS WILD-TYPE   92    9
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                2                 92
  1                0                  9
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     6  10
  19P LOSS WILD-TYPE  70 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6   10
  19P LOSS WILD-TYPE   70  202
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                6                 70
  MALE                 10                202
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
D69V10, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 52 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6793         TCGA-G7-6795 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-SX-A71S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-Y8-A8RY 
"19P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     0
  19P LOSS WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           3    13
  19P LOSS WILD-TYPE                        58   191
D69V11, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       3                 58
  WHITE                                          13                191
[1] 4 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
  19P LOSS MUTATED     0  15
  19P LOSS WILD-TYPE  12 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   15
  19P LOSS WILD-TYPE   12  225
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               15                225
[1] 2 2
[1] FALSE

Clustering(70) Variable = 19Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    10   5
  19Q LOSS WILD-TYPE 231  39
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                270 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 39 
$`19Q LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-A4-7286 TCGA-A4-8310 
       12.99        11.87        54.64        51.52        18.21        25.64 
TCGA-B1-7332 TCGA-BQ-5891 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD 
       37.51         0.95        10.68         4.01        25.84        16.90 
TCGA-IA-A40Y TCGA-Q2-A5QZ TCGA-UZ-A9PN 
        2.04        14.07        37.35 

$`19Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       21.86        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
        4.57        91.73        56.81        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       71.80        62.93        43.04        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 
        7.82         0.23        16.64        30.48        29.46        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       67.73         2.20        41.13        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       25.35        10.82         7.66         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 
       51.19        74.60        34.19        19.00        24.89        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        71.44        25.15        20.52        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       23.08        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.95               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             54.64             194.79 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            16.900             25.465 
[1] "0.9 - 54.6 (16.9)"  "0.1 - 194.8 (25.5)"
[1] "hr=" "4"  
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         2        1        10        1
  19Q LOSS WILD-TYPE     169       20        42       14
D70V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  2                169
  STAGE II                 1                 20
  STAGE III               10                 42
  STAGE IV                 1                 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
  19Q LOSS MUTATED     3   1    11
  19Q LOSS WILD-TYPE 188  32    51
D70V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                   3                188
  T2                   1                 32
  T3+T4               11                 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                 N0 N1 N2
  19Q LOSS MUTATED    1  3  1
  19Q LOSS WILD-TYPE 48 21  3
D70V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                1                 48
  N1                3                 21
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  0
  19Q LOSS WILD-TYPE 93  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    0
  19Q LOSS WILD-TYPE   93    9
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                1                 93
  1                0                  9
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     6   9
  19Q LOSS WILD-TYPE  70 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    9
  19Q LOSS WILD-TYPE   70  203
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                6                 70
  MALE                  9                203
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
D70V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     0
  19Q LOSS WILD-TYPE                                2     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           4    11
  19Q LOSS WILD-TYPE                        57   193
D70V11, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       4                 57
  WHITE                                          11                193
[1] 4 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
  19Q LOSS MUTATED     0  14
  19Q LOSS WILD-TYPE  12 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   14
  19Q LOSS WILD-TYPE   12  226
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               14                226
[1] 2 2
[1] FALSE

Clustering(71) Variable = 21Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    34   8
  21Q LOSS WILD-TYPE 207  36
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                243 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 36 
$`21Q LOSS MUTATED`
TCGA-2Z-A9JT TCGA-A4-7288 TCGA-AL-3468 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-DZ-6134 
       22.49        61.05        76.64        11.87        19.23        61.02 
TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-2Z-A9J6 TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-4A-A93X 
       84.89        17.75        56.91        51.52        30.71        12.82 
TCGA-5P-A9JY TCGA-5P-A9K9 TCGA-A4-8516 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       49.58        19.36         0.76        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-4114 TCGA-B9-A5W8 TCGA-BQ-5875 
       15.75        33.83        29.03        28.18        17.23        86.76 
TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7061 TCGA-F9-A4JJ 
       30.28        10.82         7.66         2.76         7.17        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-GL-7966 TCGA-GL-A9DC TCGA-HE-7130 
       13.08         4.01        71.44         3.68        12.89        58.19 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GE TCGA-KV-A74V TCGA-UZ-A9PN TCGA-UZ-A9PP 
       16.80         2.04        29.10        11.41        37.35        98.96 

$`21Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ 
       12.26        67.17        21.37         0.89        12.99        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-BQ-5886 
       21.67        27.68        21.07        10.16        21.86        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-GL-A59T 
       24.46        13.78         3.75        14.63         3.02        17.95 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO 
       67.17        16.34        12.13        29.26        19.73        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J7 
        7.04        75.55        59.01        58.22       100.27         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO 
       91.73        56.81        54.64        38.99        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
       29.36         5.29         0.13        11.57       106.55        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A6HP 
       19.63        19.73        14.33        12.46         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 
       20.32        30.58        34.49        12.46        50.50        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 
       20.61         0.46         1.15        43.99        22.06         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        12.30        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
       25.35         0.95         7.92       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
       61.28        50.40        49.84         7.63         7.04         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       19.00        24.89         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       90.90        11.05        39.25        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DD TCGA-GL-A9DE 
       12.92        27.65         1.05        12.43        11.21        16.31 
TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       81.93        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-MH-A55W 
       12.36        12.76        10.55        10.09        18.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PQ 
       18.02        26.20       117.40       103.63       125.29        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.76               0.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             98.96             194.79 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             18.49              25.64 
[1] "0.8 - 99.0 (18.5)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "1.6"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        17        3        14        5
  21Q LOSS WILD-TYPE     154       18        38       10
D71V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 17                154
  STAGE II                 3                 18
  STAGE III               14                 38
  STAGE IV                 5                 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
  21Q LOSS MUTATED    18   6    19
  21Q LOSS WILD-TYPE 173  27    43
D71V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                  18                173
  T2                   6                 27
  T3+T4               19                 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                 N0 N1 N2
  21Q LOSS MUTATED    6  6  2
  21Q LOSS WILD-TYPE 43 18  2
D71V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                6                 43
  N1                6                 18
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   11  3
  21Q LOSS WILD-TYPE 83  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     11    3
  21Q LOSS WILD-TYPE   83    6
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               11                 83
  1                3                  6
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    16  27
  21Q LOSS WILD-TYPE  60 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     16   27
  21Q LOSS WILD-TYPE   60  185
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               16                 60
  MALE                 27                185
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, continuous
D71V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     1
  21Q LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           5    34
  21Q LOSS WILD-TYPE                        56   170
D71V11, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       5                 56
  WHITE                                          34                170
[1] 4 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
  21Q LOSS MUTATED     1  37
  21Q LOSS WILD-TYPE  11 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   37
  21Q LOSS WILD-TYPE   11  203
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               37                203
[1] 2 2
[1] FALSE

Clustering(72) Variable = 22Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    45  15
  22Q LOSS WILD-TYPE 196  29
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                60                225 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 29 
$`22Q LOSS MUTATED`
TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47O TCGA-B9-A44B 
       12.26        61.05        12.99        49.25        27.68        11.87 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-Y8-A8RZ TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X 
       26.27        20.12         6.74        54.64        51.52        12.82 
TCGA-5P-A9JY TCGA-5P-A9KC TCGA-A4-7286 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-A5Y0 
       49.58        12.39        18.21        29.46        19.63         8.28 
TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5875 
        9.63        37.51        33.83        29.03        17.23        86.76 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5891 
        8.88        22.92        26.04        30.28         7.66         0.95 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7061 TCGA-DZ-6131 
        2.76       123.62        61.28        50.40         7.17        79.86 
TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 
       19.00        10.68        13.08         1.18         4.01        11.05 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y 
       25.15        20.52        25.84        23.08         3.68         2.04 
TCGA-J7-8537 TCGA-MH-A856 TCGA-P4-A5EA TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A7SL 
       10.55        31.13         6.61        78.90        14.07        27.06 
TCGA-SX-A7SM TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-AB4C TCGA-Y8-A896 
       11.93        18.02        37.35        86.27        39.06        18.64 

$`22Q LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M 
       22.49        67.17        21.37         0.89        76.64        21.67 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       21.07        10.16        21.86        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       11.97        96.92        44.84        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-2K-A9WE 
       62.83        86.37        21.60        15.91        15.62         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       91.73        56.81        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
       29.36         5.29         0.13        11.57       106.55        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 
       19.36        12.99        27.09        67.43        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 
       25.64        23.97        23.28        23.31         0.76        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
        2.20        41.13        36.49        20.25        16.77        20.32 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 
       20.61         0.46         1.15        43.99        22.06         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
       14.86        17.49        12.30        19.27        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5893 
       47.80        21.63        40.83        25.35        10.82         7.92 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
       48.26        93.34        49.84         7.63         7.04         3.81 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       40.77        80.88        51.19        74.60        34.19        24.89 
TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        2.40         0.43        51.78        90.90        39.25        71.44 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       20.25        17.62        15.48        99.78        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-SX-A71R 
       99.12        92.58        52.27        16.01        50.60        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       49.45        44.61        28.80        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
      125.29        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A897 
      110.73        51.35        31.73        26.01        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.95               0.10 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            123.62             194.79 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            19.875             26.010 
[1] "0.9 - 123.6 (19.9)" "0.1 - 194.8 (26.0)"
[1] "hr=" "2.7"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED        20        3        25        8
  22Q LOSS WILD-TYPE     151       18        27        7
D72V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 20                151
  STAGE II                 3                 18
  STAGE III               25                 27
  STAGE IV                 8                  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
  22Q LOSS MUTATED    24   5    31
  22Q LOSS WILD-TYPE 167  28    31
D72V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                  24                167
  T2                   5                 28
  T3+T4               31                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  22Q LOSS MUTATED   11 14  2
  22Q LOSS WILD-TYPE 38 10  2
D72V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               11                 38
  N1               14                 10
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   21  5
  22Q LOSS WILD-TYPE 73  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     21    5
  22Q LOSS WILD-TYPE   73    4
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               21                 73
  1                5                  4
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    27  33
  22Q LOSS WILD-TYPE  49 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     27   33
  22Q LOSS WILD-TYPE   49  179
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               27                 49
  MALE                 33                179
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, continuous
D72V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0     3
  22Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          12    43
  22Q LOSS WILD-TYPE                        49   161
D72V11, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                      12                 49
  WHITE                                          43                161
[1] 4 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
  22Q LOSS MUTATED     3  46
  22Q LOSS WILD-TYPE   9 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   46
  22Q LOSS WILD-TYPE    9  194
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               46                194
[1] 2 2
[1] FALSE

Clustering(73) Variable = XP LOSS MUTATION ANALYSIS
D73V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    20  13
  XP LOSS WILD-TYPE 221  31
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               33               252 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               13                31 
$`XP LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-B9-5155 TCGA-B9-A44B TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       12.99        21.86        11.87        91.73        54.64        51.52 
TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-7286 
       12.82        15.48        71.80        43.04        67.43        18.21 
TCGA-A4-7287 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5876 
       19.63         9.63        37.51        29.03        20.61        19.27 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-DZ-6131 TCGA-F9-A4JJ 
        8.88        22.92        21.63        25.35        79.86        10.68 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 
       13.08         0.43        11.05        20.52        16.90        10.55 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       14.07        18.02        86.27 

$`XP LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE 
       86.37        21.60        15.91        15.62         6.74         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       56.81        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        5.29         0.13        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       22.26        78.64        62.93        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       27.09         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 
       14.86        17.49        12.30        86.76        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 
       47.80        40.83        26.04        30.28        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
        3.81        40.77        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
       19.00        24.89         2.40         1.18         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
       90.90        39.25        71.44        25.15        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        23.08        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 
       96.69        22.26        21.34        12.36        12.76        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.43              0.10 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            91.73            194.79 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           19.630            26.025 
[1] "0.4 - 91.7 (19.6)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "3.9"
D73V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED         7        1        15        4
  XP LOSS WILD-TYPE     164       20        37       11
D73V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 7               164
  STAGE II                1                20
  STAGE III              15                37
  STAGE IV                4                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
  XP LOSS MUTATED    10   4    19
  XP LOSS WILD-TYPE 181  29    43
D73V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T1                 10               181
  T2                  4                29
  T3+T4              19                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                N0 N1 N2
  XP LOSS MUTATED    5  9  1
  XP LOSS WILD-TYPE 44 15  3
D73V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0               5                44
  N1               9                15
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    8  2
  XP LOSS WILD-TYPE 86  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      8    2
  XP LOSS WILD-TYPE   86    7
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0               8                86
  1               2                 7
[1] 2 2
[1] FALSE
D73V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    13  20
  XP LOSS WILD-TYPE  63 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     13   20
  XP LOSS WILD-TYPE   63  192
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              13                63
  MALE                20               192
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, continuous
D73V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     3
  XP LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                           9    20
  XP LOSS WILD-TYPE                        52   184
D73V11, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                      9                52
  WHITE                                         20               184
[1] 4 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
  XP LOSS MUTATED     0  26
  XP LOSS WILD-TYPE  12 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   26
  XP LOSS WILD-TYPE   12  214
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              26               214
[1] 2 2
[1] FALSE

Clustering(74) Variable = XQ LOSS MUTATION ANALYSIS
D74V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    16  13
  XQ LOSS WILD-TYPE 225  31
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               29               256 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               13                31 
$`XQ LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-B9-5155 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X 
       12.99        21.86        91.73        54.64        51.52        12.82 
TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-3466 
       15.48        43.04        67.43        18.21        19.63         9.63 
TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
       37.51        29.03        19.27         8.88        22.92        21.63 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6793 TCGA-G7-7501 
       79.86        10.68        13.08         0.43        11.05        20.52 
TCGA-G7-A8LD TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       16.90        10.55        14.07        18.02        86.27 

$`XQ LOSS WILD-TYPE`
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
        4.57        56.81        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
       29.36         5.29         0.13        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 
       90.21        22.26        78.64        71.80        62.93        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       12.99        12.39        27.09         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       67.73         2.20        41.13        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       86.76        63.72        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        2.40         1.18         4.01        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       71.44        25.15        25.84        25.25        17.98        23.08 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        12.36        12.76        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       78.90        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.43              0.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            91.73            194.79 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            19.27             26.01 
[1] "0.4 - 91.7 (19.3)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "4.5"
D74V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         7        1        13        4
  XQ LOSS WILD-TYPE     164       20        39       11
D74V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 7               164
  STAGE II                1                20
  STAGE III              13                39
  STAGE IV                4                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 LOSS MUTATED     9   3    17
  XQ LOSS WILD-TYPE 182  30    45
D74V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                  9               182
  T2                  3                30
  T3+T4              17                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                N0 N1 N2
  XQ LOSS MUTATED    4  9  1
  XQ LOSS WILD-TYPE 45 15  3
D74V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0               4                45
  N1               9                15
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    7  2
  XQ LOSS WILD-TYPE 87  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      7    2
  XQ LOSS WILD-TYPE   87    7
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               7                87
  1               2                 7
[1] 2 2
[1] FALSE
D74V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    12  17
  XQ LOSS WILD-TYPE  64 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12   17
  XQ LOSS WILD-TYPE   64  195
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              12                64
  MALE                17               195
[1] 2 2
[1] FALSE
D74V8, continuous
D74V9, continuous
D74V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     3
  XQ LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           7    18
  XQ LOSS WILD-TYPE                        54   186
D74V11, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                      7                54
  WHITE                                         18               186
[1] 4 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
  XQ LOSS MUTATED     0  23
  XQ LOSS WILD-TYPE  12 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   23
  XQ LOSS WILD-TYPE   12  217
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              23               217
[1] 2 2
[1] FALSE
