[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/15081779/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/15087099/transformed.cor.cli.txt"

nPatients in clinical file=271, in cluster file=288, common to both=269
[1] "Reduce the number of clustering variables from 82 to 73."
[1]  73 269
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8               261 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8               261 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16               253 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16               253 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               40               229 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               40               229 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               45               224 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               45               224 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               70               199 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               70               199 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               88               181 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               88               181 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               259 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               259 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               260 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               260 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               32               237 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               32               237 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               30               239 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               30               239 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               259 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               259 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               261 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               261 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              161               108 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              161               108 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              162               107 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              162               107 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18               251 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18               251 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23               246 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23               246 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               266 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               266 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                261 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                261 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                261 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                261 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                258 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                258 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                259 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                259 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               107                162 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               107                162 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               107                162 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               107                162 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                26                243 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                26                243 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                266 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                266 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                264 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                264 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               143                126 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               143                126 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               139                130 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               139                130 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               165                104 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               165                104 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               180                 89 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               180                 89 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                257 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                257 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                260 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                260 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                265 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                265 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                265 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                265 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                91                178 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                91                178 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                93                176 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                93                176 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                250 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                250 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                266 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                266 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               82               187 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               82               187 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               85               184 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               85               184 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               26               243 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               26               243 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               19               250 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               19               250 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3               266 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3               266 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21               248 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21               248 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               263 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               263 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               246 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               23               246 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               24               245 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               24               245 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               261 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               261 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8               261 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8               261 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19               250 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19               250 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               24               245 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               24               245 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13               256 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13               256 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7               262 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7               262 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               32               237 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               32               237 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               32               237 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               32               237 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                255 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                255 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                254 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                254 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                16                253 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                16                253 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                20                249 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                20                249 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                246 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                246 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                44                225 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                44                225 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                29                240 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                29                240 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                265 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                265 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                262 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                262 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                261 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                261 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                39                230 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                39                230 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                42                227 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                42                227 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                15                254 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                15                254 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                254 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                254 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                41                228 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                41                228 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                212 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                212 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               30               239 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               30               239 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               27               242 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               27               242 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 269 columns.

[1] "Batch" "22"   
[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=35,	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=219,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=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:'DCC_UPLOAD_DATE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'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 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=26,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 269 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"                "NEOPLASM_DISEASESTAGE"        
 [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
NEOPLASM_DISEASESTAGE, 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 
176  29  54   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  176    29    56 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
176  29  54   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  176    29    56 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
45 22  4 
[1] "table(vv)"
vv
N0 N1 N2 
45 22  4 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
45 22  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
45 22  4 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=34, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=33, 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     3   4
  1P GAIN WILD-TYPE 219  30
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7               249 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                30 
$`1P GAIN MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-BQ-5893 TCGA-G7-6789 TCGA-GL-7966 TCGA-IA-A40Y 
       12.99        49.25         7.92         4.01         3.68         2.04 
TCGA-WN-A9G9 
       26.01 

$`1P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       13.68        25.84         6.38        17.98        17.33        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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C 
       52.11        30.67        25.68        27.39        12.99        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2.04              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            49.25            194.79 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             7.92             21.63 
[1] "2.0 - 49.2 (7.9)"   "0.1 - 194.8 (21.6)"
[1] "hr=" "11" 
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         1        0         5        2
  1P GAIN WILD-TYPE     166       21        44       12
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 1               166
  STAGE II                0                21
  STAGE III               5                44
  STAGE IV                2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  1P GAIN MUTATED     2   0     6
  1P GAIN WILD-TYPE 174  29    50
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1                  2               174
  T2                  0                29
  T3+T4               6                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
  1P GAIN MUTATED    0  4  1
  1P GAIN WILD-TYPE 45 18  3
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               0                45
  N1               4                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"
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  1
  1P GAIN WILD-TYPE 89  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    1
  1P GAIN WILD-TYPE   89    8
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               1                89
  1               1                 8
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5   3
  1P GAIN WILD-TYPE  67 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5    3
  1P GAIN WILD-TYPE   67  194
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               5                67
  MALE                 3               194
[1] 2 2
[1] FALSE
D1V8, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                59 
       TCGA-2Z-A9JK        TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7286 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT        TCGA-A4-A57E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-J7-8537 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V9, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                64 
       TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9JD        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-2Z-A9JQ        TCGA-4A-A93W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-8310        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-3466        TCGA-AL-3472        TCGA-AL-7173 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4115        TCGA-B9-4117        TCGA-B9-7268 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7834 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501        TCGA-G7-A8LB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"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-IZ-A6M8        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-PJ-A5Z9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY        TCGA-Y8-A8RZ 
"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 
                1                50 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7963        TCGA-F9-A97G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-UZ-A9PS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-Y8-A8RY        TCGA-Y8-A8RZ 
"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     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0     7
  1P GAIN WILD-TYPE                        60   180
D1V11, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                60
  WHITE                                          7               180
[1] 4 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   7
  1P GAIN WILD-TYPE  12 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    7
  1P GAIN WILD-TYPE   12  213
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               7               213
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED     8   7
  1Q GAIN WILD-TYPE 214  27
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15               241 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                7                27 
$`1Q GAIN MUTATED`
TCGA-2Z-A9J2 TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-BQ-5885 
       59.01        19.63        12.99         9.63        49.25        30.28 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-G7-6789 TCGA-G7-A8LD 
       25.35         7.66         0.95         7.92         4.01        16.90 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-WN-A9G9 
        3.68         2.04        26.01 

$`1Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        18.21        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         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-3468 TCGA-AL-3471 
       15.75         8.28        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       30.35        25.08        44.61         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         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-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       21.63        40.83        26.04        26.04        13.25        10.88 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        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 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        17.33        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       25.68        27.39        12.99        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       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 
            12.99             21.67 
[1] "0.9 - 59.0 (13.0)"  "0.1 - 194.8 (21.7)"
[1] "hr=" "7.5"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         3        0        10        3
  1Q GAIN WILD-TYPE     164       21        39       11
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 3               164
  STAGE II                0                21
  STAGE III              10                39
  STAGE IV                3                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
  1Q GAIN MUTATED     4   0    12
  1Q GAIN WILD-TYPE 172  29    44
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                  4               172
  T2                  0                29
  T3+T4              12                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  1Q GAIN MUTATED    4  6  1
  1Q GAIN WILD-TYPE 41 16  3
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0               4                41
  N1               6                16
  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"
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    5  2
  1Q GAIN WILD-TYPE 85  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5    2
  1Q GAIN WILD-TYPE   85    7
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               5                85
  1               2                 7
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     8   8
  1Q GAIN WILD-TYPE  64 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8    8
  1Q GAIN WILD-TYPE   64  189
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               8                64
  MALE                 8               189
[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                49 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7963        TCGA-F9-A97G 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LE        TCGA-GL-7773 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-PJ-A5Z9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        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" 
       TCGA-Y8-A8RZ 
"1Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           0    15
  1Q GAIN WILD-TYPE                        60   172
D2V11, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                60
  WHITE                                         15               172
[1] 4 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  14
  1Q GAIN WILD-TYPE  12 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   14
  1Q GAIN WILD-TYPE   12  206
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              14               206
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    34   6
  2P GAIN WILD-TYPE 188  28
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               40               216 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                28 
$`2P GAIN MUTATED`
TCGA-2Z-A9J5 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3466 
      100.27        16.96         8.48        16.31        15.75         9.63 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B 
       13.55         2.20         7.33        10.16         0.46         2.10 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 
       11.97         7.92         2.76        96.92        13.61        51.19 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A8LC TCGA-GL-7966 
        1.18         4.01        51.78        39.25        17.33         3.68 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD 
       17.95        68.12        11.84        16.80         2.04        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-PJ-A5Z9 
       29.10        11.41        34.29        42.94        84.95        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UZ-A9PK 
       14.07        28.80        41.62        60.03 

$`2P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-A5Y0 TCGA-A4-A5Y1 
       19.63        19.73        14.33        12.46         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        58.45        76.64        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       49.25        19.56        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
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-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
       10.88         7.66         0.95       123.62        48.26        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
       14.63         3.02        40.77        79.86        80.88        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
        2.40         0.43        48.62        11.05        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       13.68        25.84         6.38        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         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       11.21         4.60        13.41        56.75        73.25         5.49 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       16.34        12.36         0.13        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       99.78        87.22         6.61        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        12.85        47.90        47.44        33.04 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR 
       27.06        11.93        19.00        38.63        16.31        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        18.02        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.46              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           100.27            194.79 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           14.910            22.705 
[1] "0.5 - 100.3 (14.9)" "0.1 - 194.8 (22.7)"
[1] "hr=" "1.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        24        3         6        6
  2P GAIN WILD-TYPE     143       18        43        8
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                24               143
  STAGE II                3                18
  STAGE III               6                43
  STAGE IV                6                 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
  2P GAIN MUTATED    24   6    10
  2P GAIN WILD-TYPE 152  23    46
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                 24               152
  T2                  6                23
  T3+T4              10                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
  2P GAIN MUTATED    5  7  1
  2P GAIN WILD-TYPE 40 15  3
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0               5                40
  N1               7                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"
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   10  5
  2P GAIN WILD-TYPE 80  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     10    5
  2P GAIN WILD-TYPE   80    4
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              10                80
  1               5                 4
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    12  28
  2P GAIN WILD-TYPE  60 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     12   28
  2P GAIN WILD-TYPE   60  169
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              12                60
  MALE                28               169
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           7    29
  2P GAIN WILD-TYPE                        53   158
D3V11, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      7                53
  WHITE                                         29               158
[1] 4 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  34
  2P GAIN WILD-TYPE  10 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   34
  2P GAIN WILD-TYPE   10  186
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              34               186
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    38   7
  2Q GAIN WILD-TYPE 184  27
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               45               211 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                27 
$`2Q GAIN MUTATED`
TCGA-2Z-A9J5 TCGA-2Z-A9JR TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
      100.27         5.29        16.96         8.48        16.31        15.75 
TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A657 
        9.63        13.55        44.61         2.20         7.33         6.58 
TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.16         0.46         2.10        11.97         7.92         2.76 
TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
       96.92        13.61        51.19         1.18         4.01        51.78 
TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF 
       39.25        25.84        17.33         3.68        17.95        68.12 
TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       11.84        16.80         2.04        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V 
       34.29        42.94        84.95        17.75        14.07        28.80 
TCGA-SX-A7SQ TCGA-UZ-A9PK TCGA-UZ-A9PQ 
       41.62        60.03        86.27 

$`2Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       29.36        25.58        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
       19.73        14.33        12.46         8.28        12.99        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 
       58.45        76.64        30.35        25.08        49.25        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40        20.61         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06        19.23         6.81         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.17         3.81        11.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 
       24.89        10.68        13.08         2.40         0.43        48.62 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       11.05        34.82        25.15        13.68         6.38        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-A5NH TCGA-HE-A5NJ 
       12.43         0.89        11.21         4.60        13.41        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       73.25         5.49        19.99        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z 
       22.26        21.34        16.34        12.36         0.13        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED 
       21.44        15.48        99.78        87.22         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        12.85        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       47.44        33.04        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM 
       16.31        26.47        48.30        43.76        18.02        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       21.93         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.46              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           100.27            194.79 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            15.75             22.49 
[1] "0.5 - 100.3 (15.8)" "0.1 - 194.8 (22.5)"
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        27        3         7        7
  2Q GAIN WILD-TYPE     140       18        42        7
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                27               140
  STAGE II                3                18
  STAGE III               7                42
  STAGE IV                7                 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
  2Q GAIN MUTATED    27   7    11
  2Q GAIN WILD-TYPE 149  22    45
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                 27               149
  T2                  7                22
  T3+T4              11                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
  2Q GAIN MUTATED    6  8  2
  2Q GAIN WILD-TYPE 39 14  2
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0               6                39
  N1               8                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"
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   12  5
  2Q GAIN WILD-TYPE 78  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     12    5
  2Q GAIN WILD-TYPE   78    4
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              12                78
  1               5                 4
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    13  32
  2Q GAIN WILD-TYPE  59 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     13   32
  2Q GAIN WILD-TYPE   59  165
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              13                59
  MALE                32               165
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           8    33
  2Q GAIN WILD-TYPE                        52   154
D4V11, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      8                52
  WHITE                                         33               154
[1] 4 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  39
  2Q GAIN WILD-TYPE  10 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   39
  2Q GAIN WILD-TYPE   10  181
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              39               181
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    58   6
  3P GAIN WILD-TYPE 164  28
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               64               192 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                28 
$`3P GAIN MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-A4-7287 TCGA-A4-8311 TCGA-A4-8516 
        7.04       100.27        56.91        19.63        23.97         0.76 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-AL-3468 
       19.73        14.33        12.46        16.96        16.31        76.64 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 
       13.55         2.20         7.33         6.58        30.58        10.16 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       28.18         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 
       17.49        47.80        26.04        48.26        96.92         7.04 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7963 
        3.81        11.61        35.93        37.55        24.46        40.77 
TCGA-DZ-6133 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LB TCGA-GL-6846 
       51.19        13.08         2.40        51.78        17.98       194.79 
TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A83S 
       17.95        11.21        68.12        11.84         5.49        85.78 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVM 
       11.97        29.10        11.41        87.22         6.61        50.60 
TCGA-PJ-A5Z9 TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS 
       17.75        28.80        19.00        16.31        41.62        48.30 
TCGA-UZ-A9PK TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-Y8-A895 
       60.03        52.11        25.68        15.91 

$`3P GAIN WILD-TYPE`
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       75.55        59.01        58.22         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       34.85        56.81        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       18.21        61.05         0.10        35.18        19.13         0.89 
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-A4-8517 TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       23.31        19.63         8.48        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       49.25        19.56        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       16.77         0.46        33.83        10.09        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       50.50        26.40        20.61         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        12.30        86.76        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-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 
       11.97         7.92         2.76       123.62        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 
        7.63         7.17        13.61       129.86        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
       14.63         3.02        79.86        80.88        61.02        54.90 
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        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       13.68        25.84         6.38        17.33        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         0.89 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
        4.60        13.41        56.75        73.25        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
        2.04        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       12.36         0.13        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       99.78        42.94        84.95        92.58        52.27        16.01 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        12.85        14.07        47.90        47.44        33.04 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 
       27.06        11.93        38.63        26.47        43.76        18.02 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PU 
       14.83        21.93         0.53        86.27        38.86        30.67 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       27.39        12.99        26.01        29.00        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         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 
           19.315            21.650 
[1] "0.5 - 194.8 (19.3)" "0.1 - 129.9 (21.6)"
[1] "hr=" "1.7"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED        50        7         6        2
  3P GAIN WILD-TYPE     117       14        43       12
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                50               117
  STAGE II                7                14
  STAGE III               6                43
  STAGE IV                2                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 GAIN MUTATED    51  10     7
  3P GAIN WILD-TYPE 125  19    49
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                 51               125
  T2                 10                19
  T3+T4               7                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
  3P GAIN MUTATED    7  2  0
  3P GAIN WILD-TYPE 38 20  4
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               7                38
  N1               2                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"
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   26  0
  3P GAIN WILD-TYPE 64  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26    0
  3P GAIN WILD-TYPE   64    9
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              26                64
  1               0                 9
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    17  53
  3P GAIN WILD-TYPE  55 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     17   53
  3P GAIN WILD-TYPE   55  144
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              17                55
  MALE                53               144
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                          12    50
  3P GAIN WILD-TYPE                        48   137
D5V11, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                     12                48
  WHITE                                         50               137
[1] 4 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  57
  3P GAIN WILD-TYPE   9 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   57
  3P GAIN WILD-TYPE    9  163
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO              57               163
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    71  11
  3Q GAIN WILD-TYPE 151  23
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               82               174 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               11                23 
$`3Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-A4-7287 
        7.04        59.01        58.22       100.27        56.91        19.63 
TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 
       30.48        23.97        23.31         0.76        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3468 TCGA-AL-3471 
       12.46        16.96        16.31        15.75        76.64        13.55 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 
        2.20         7.33         6.58        30.58        10.16        28.18 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7045 TCGA-BQ-7046 
       17.49        47.80        26.04         7.66        48.26        96.92 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7963 
        7.04         3.81        35.93        37.55        24.46        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       80.88        51.19        54.90        34.19        13.08         2.40 
TCGA-G7-6790 TCGA-G7-A8LB TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A59T TCGA-GL-A9DD 
       51.78        17.98        16.90       194.79        17.95        11.21 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A83S TCGA-IA-A83W TCGA-KV-A6GD 
       68.12        11.84         5.49        85.78        67.17        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVL 
       29.10        11.41        99.78        87.22         6.61        16.01 
TCGA-P4-AAVM TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP 
       50.60        17.75        14.07        28.80        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS 
       41.62        48.30        60.03        14.83        21.93        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-Y8-A895 
       30.67        25.68        12.99        15.91 

$`3Q GAIN WILD-TYPE`
TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       75.55         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 
       22.49         0.13        12.82        11.57        18.21        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8517 TCGA-A4-A57E TCGA-A4-A5Y0 
       29.46        25.64        23.28        19.63         8.48         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       44.61        49.25        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 
        3.55        16.77         0.46        33.83        10.09        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W7 TCGA-B9-A5W8 
       12.46        50.50        26.40        20.61        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        12.30        86.76        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-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 
       30.28        25.35        13.25        10.88         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        7.92         2.76       123.62        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 
        7.17        11.61        13.61       129.86        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 
       14.63         3.02        79.86        61.02        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       10.68         1.18         0.43         4.01        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       17.33        80.65        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK 
       12.43         0.89         4.60        13.41        56.75        73.25 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-8196 
       16.80        19.99         2.04        88.24        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       16.34        12.36         0.13        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVO 
       15.48        42.94        84.95        92.58        52.27        78.90 
TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM 
       12.85        47.90        47.44        33.04        27.06        11.93 
TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       38.63        26.47        43.76        18.02         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PX TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       38.86        27.39        26.01        29.00        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         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 
            20.83             21.39 
[1] "0.5 - 194.8 (20.8)" "0.1 - 129.9 (21.4)"
[1] "hr=" "1.2"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        58       10        12        2
  3Q GAIN WILD-TYPE     109       11        37       12
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                58               109
  STAGE II               10                11
  STAGE III              12                37
  STAGE IV                2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  3Q GAIN MUTATED    60  13    12
  3Q GAIN WILD-TYPE 116  16    44
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                 60               116
  T2                 13                16
  T3+T4              12                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  3Q GAIN MUTATED   10  4  0
  3Q GAIN WILD-TYPE 35 18  4
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              10                35
  N1               4                18
  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"
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   29  0
  3Q GAIN WILD-TYPE 61  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     29    0
  3Q GAIN WILD-TYPE   61    9
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              29                61
  1               0                 9
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    20  68
  3Q GAIN WILD-TYPE  52 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     20   68
  3Q GAIN WILD-TYPE   52  129
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              20                52
  MALE                68               129
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          15    62
  3Q GAIN WILD-TYPE                        45   125
D6V11, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                     15                45
  WHITE                                         62               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"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     4  71
  3Q GAIN WILD-TYPE   8 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4   71
  3Q GAIN WILD-TYPE    8  149
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO              71               149
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     7   2
  4P GAIN WILD-TYPE 215  32
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               247 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                32 
$`4P GAIN MUTATED`
TCGA-AL-3466 TCGA-B9-4114 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-G7-6789 TCGA-G7-6795 
        9.63        28.18         0.16        11.97         4.01        39.25 
TCGA-G7-A8LC TCGA-SX-A7SR TCGA-WN-AB4C 
       17.33        26.47        29.00 

$`4P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06         2.10        19.23         6.81        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        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-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 
       25.68        27.39        12.99        26.01        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.16              0.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            39.25            194.79 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            17.33             21.44 
[1] "0.2 - 39.2 (17.3)"  "0.1 - 194.8 (21.4)"
[1] "hr=" "3.3"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         6        1         0        2
  4P GAIN WILD-TYPE     161       20        49       12
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 6               161
  STAGE II                1                20
  STAGE III               0                49
  STAGE IV                2                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
  4P GAIN MUTATED     6   2     2
  4P GAIN WILD-TYPE 170  27    54
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                  6               170
  T2                  2                27
  T3+T4               2                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
  4P GAIN MUTATED    2  1  1
  4P GAIN WILD-TYPE 43 21  3
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               2                43
  N1               1                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"
D7V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 88  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   88    8
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               2                88
  1               1                 8
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2   8
  4P GAIN WILD-TYPE  70 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    8
  4P GAIN WILD-TYPE   70  189
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                70
  MALE                 8               189
[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     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1     9
  4P GAIN WILD-TYPE                        59   178
D7V11, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                59
  WHITE                                          9               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"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  10
  4P GAIN WILD-TYPE  12 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   10
  4P GAIN WILD-TYPE   12  210
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              10               210
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     7   1
  4Q GAIN WILD-TYPE 215  33
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               248 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                33 
$`4Q GAIN MUTATED`
TCGA-B9-4114 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A8LC 
       28.18         0.16        11.97         4.01        39.25        17.33 
TCGA-SX-A7SR TCGA-WN-AB4C 
       26.47        29.00 

$`4Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
       43.99        22.06         2.10        19.23         6.81        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        48.62        11.05        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       16.31        41.62        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-Y8-A894 
       30.67        25.68        27.39        12.99        26.01        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.16              0.10 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            39.25            194.79 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            21.90             21.39 
[1] "0.2 - 39.2 (21.9)"  "0.1 - 194.8 (21.4)"
[1] "hr=" "1.6"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         6        1         0        1
  4Q GAIN WILD-TYPE     161       20        49       13
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 6               161
  STAGE II                1                20
  STAGE III               0                49
  STAGE IV                1                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
  4Q GAIN MUTATED     6   2     1
  4Q GAIN WILD-TYPE 170  27    55
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                  6               170
  T2                  2                27
  T3+T4               1                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
  4Q GAIN MUTATED    2  0  1
  4Q GAIN WILD-TYPE 43 22  3
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               2                43
  N1               0                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"
D8V6, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    2  0
  4Q GAIN WILD-TYPE 88  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    0
  4Q GAIN WILD-TYPE   88    9
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               2                88
  1               0                 9
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2   7
  4Q GAIN WILD-TYPE  70 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    7
  4Q GAIN WILD-TYPE   70  190
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                70
  MALE                 7               190
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                58 
       TCGA-2Z-A9JK        TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7286 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT        TCGA-A4-A57E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-SX-A7SU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V9, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                63 
       TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-2Z-A9JD        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JQ        TCGA-4A-A93W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4115        TCGA-B9-4117        TCGA-B9-7268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7834 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501        TCGA-G7-A8LB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RY        TCGA-Y8-A8RZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           1     8
  4Q GAIN WILD-TYPE                        59   179
D8V11, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                59
  WHITE                                          8               179
[1] 4 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  12 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    9
  4Q GAIN WILD-TYPE   12  211
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               9               211
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    25   5
  5P GAIN WILD-TYPE 197  29
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               30               226 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                29 
$`5P GAIN MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J3 TCGA-4A-A93X TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D 
        7.04        58.22        12.82        29.46         0.76        12.46 
TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 
        8.48         9.63        25.08        19.56         0.46         0.46 
TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-7838 TCGA-DZ-6131 
        0.16        25.35         0.95        11.97        24.46        79.86 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-A5NK 
       19.00        13.08         4.01        17.33         1.05        73.25 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5EB TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A7SQ 
        2.04        11.97        84.95        16.01        14.07        41.62 

$`5P GAIN WILD-TYPE`
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        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
        0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
       16.31        15.75         8.28        12.99        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       76.64        13.55        30.35        44.61        49.25         2.20 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
       10.16        50.50        28.18        26.40        20.61         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
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-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.88         7.66 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        24.89        10.68         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        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       25.15        13.68        25.84         6.38        17.98        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R 
       80.65       194.79        12.92         3.68        27.65        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       11.84        56.75         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       52.27        50.60        78.90        12.85        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       38.63        16.31        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.16              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            84.95            194.79 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           12.950            22.375 
[1] "0.2 - 85.0 (12.9)"  "0.1 - 194.8 (22.4)"
[1] "hr=" "2"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED        14        3         8        3
  5P GAIN WILD-TYPE     153       18        41       11
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                14               153
  STAGE II                3                18
  STAGE III               8                41
  STAGE IV                3                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    15   5    10
  5P GAIN WILD-TYPE 161  24    46
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                 15               161
  T2                  5                24
  T3+T4              10                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
  5P GAIN MUTATED    8  2  1
  5P GAIN WILD-TYPE 37 20  3
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0               8                37
  N1               2                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"
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   13  2
  5P GAIN WILD-TYPE 77  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     13    2
  5P GAIN WILD-TYPE   77    7
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              13                77
  1               2                 7
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     7  25
  5P GAIN WILD-TYPE  65 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   25
  5P GAIN WILD-TYPE   65  172
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                65
  MALE                25               172
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           4    24
  5P GAIN WILD-TYPE                        56   163
D9V11, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      4                56
  WHITE                                         24               163
[1] 4 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  25
  5P GAIN WILD-TYPE  11 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   25
  5P GAIN WILD-TYPE   11  195
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              25               195
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    25   3
  5Q GAIN WILD-TYPE 197  31
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               28               228 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                31 
$`5Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-4A-A93X TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E 
        7.04        12.82        29.46         0.76        12.46         8.48 
TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 
        9.63        25.08        19.56         0.46         0.46         0.16 
TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-7838 TCGA-EV-5902 TCGA-F9-A7Q0 
       25.35         0.95        11.97        24.46        19.00        13.08 
TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40Y TCGA-KV-A6GD 
        4.01        17.33         1.05        73.25         2.04        11.97 
TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
       99.78        84.95        14.07        41.62 

$`5Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
       19.13         0.89         0.23        16.64        30.48        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
       16.96        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ 
       58.45        76.64        13.55        30.35        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        2.20         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        6.81        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-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        7.66         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 
       11.61        13.61       129.86        35.93        37.55        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        61.02        54.90        34.19        24.89        10.68 
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        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       68.12        13.41        11.84        56.75         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36         0.13        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       25.97        21.44        15.48        87.22        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        38.63        16.31        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         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 
           12.640            22.375 
[1] "0.2 - 99.8 (12.6)"  "0.1 - 194.8 (22.4)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED        14        2         8        3
  5Q GAIN WILD-TYPE     153       19        41       11
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                14               153
  STAGE II                2                19
  STAGE III               8                41
  STAGE IV                3                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     9
  5Q GAIN WILD-TYPE 160  25    47
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                 16               160
  T2                  4                25
  T3+T4               9                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
  5Q GAIN MUTATED    7  3  1
  5Q GAIN WILD-TYPE 38 19  3
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               7                38
  N1               3                19
  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"
D10V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   13  2
  5Q GAIN WILD-TYPE 77  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     13    2
  5Q GAIN WILD-TYPE   77    7
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              13                77
  1               2                 7
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7  23
  5Q GAIN WILD-TYPE  65 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   23
  5Q GAIN WILD-TYPE   65  174
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               7                65
  MALE                23               174
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           5    21
  5Q GAIN WILD-TYPE                        55   166
D10V11, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      5                55
  WHITE                                         21               166
[1] 4 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  25
  5Q GAIN WILD-TYPE  12 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   25
  5Q GAIN WILD-TYPE   12  195
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              25               195
[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 217  29
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               246 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5                29 
$`6P GAIN MUTATED`
TCGA-4A-A93X TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B9-A69E TCGA-BQ-5893 TCGA-BQ-7048 
       12.82         9.63        49.25        14.86         7.92        93.34 
TCGA-DW-5561 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
       13.61         6.61        14.07        86.27 

$`6P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
       16.31        15.75         8.28        12.99        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
        2.10        19.23         6.81         0.16        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-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
        7.04         7.17         3.81        11.61       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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
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        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       21.44        15.48        99.78        87.22        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
        0.53        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         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             21.65 
[1] "6.6 - 93.3 (13.8)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "3.5"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         1        0         6        2
  6P GAIN WILD-TYPE     166       21        43       12
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 1               166
  STAGE II                0                21
  STAGE III               6                43
  STAGE IV                2                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     7
  6P GAIN WILD-TYPE 175  28    49
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                  1               175
  T2                  1                28
  T3+T4               7                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
  6P GAIN MUTATED    1  4  0
  6P GAIN WILD-TYPE 44 18  4
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               1                44
  N1               4                18
  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 88  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    2
  6P GAIN WILD-TYPE   88    7
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               2                88
  1               2                 7
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3   7
  6P GAIN WILD-TYPE  69 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    7
  6P GAIN WILD-TYPE   69  190
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               3                69
  MALE                 7               190
[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     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           3     7
  6P GAIN WILD-TYPE                        57   180
D11V11, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      3                57
  WHITE                                          7               180
[1] 4 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  12 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   10
  6P GAIN WILD-TYPE   12  210
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              10               210
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     3   5
  6Q GAIN WILD-TYPE 219  29
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               248 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                29 
$`6Q GAIN MUTATED`
TCGA-4A-A93X TCGA-AL-3466 TCGA-AL-A5DJ TCGA-BQ-5893 TCGA-DW-5561 TCGA-P4-A5EA 
       12.82         9.63        49.25         7.92        13.61         6.61 
TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
       14.07        86.27 

$`6Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
       16.31        15.75         8.28        12.99        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        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 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        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         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        12.85        17.75        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       14.83        21.93         0.53        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
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 
            86.27            194.79 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           13.215            21.650 
[1] "6.6 - 86.3 (13.2)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "6"  
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         1        0         4        2
  6Q GAIN WILD-TYPE     166       21        45       12
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 1               166
  STAGE II                0                21
  STAGE III               4                45
  STAGE IV                2                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   1     5
  6Q GAIN WILD-TYPE 175  28    51
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1                  1               175
  T2                  1                28
  T3+T4               5                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
  6Q GAIN MUTATED    0  4  0
  6Q GAIN WILD-TYPE 45 18  4
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0               0                45
  N1               4                18
  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 89  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    2
  6Q GAIN WILD-TYPE   89    7
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               1                89
  1               2                 7
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3   5
  6Q GAIN WILD-TYPE  69 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    5
  6Q GAIN WILD-TYPE   69  192
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                69
  MALE                 5               192
[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                49 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD 
"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-B9-4117 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-PJ-A5Z9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-UZ-A9PR        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" 
       TCGA-Y8-A8RZ 
"6Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     0
  6Q GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           3     5
  6Q GAIN WILD-TYPE                        57   182
D12V11, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      3                57
  WHITE                                          5               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"
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0   8
  6Q GAIN WILD-TYPE  12 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    8
  6Q GAIN WILD-TYPE   12  212
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               8               212
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   135  15
  7P GAIN WILD-TYPE  87  19
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              150               106 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15                19 
$`7P GAIN MUTATED`
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-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       34.85        56.81        26.43        30.71        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7288 
        5.29        16.18        22.49         0.13        12.82        61.05 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
       19.13         0.89        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-3468 TCGA-AL-3471 TCGA-AL-3472 
       16.31        15.75        12.46        76.64        13.55        30.35 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61        49.25         2.20        21.67        24.56         3.55 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 
        0.46         6.58        33.83        30.58        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.18        26.40         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 
       43.99        22.06        19.23        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        10.88         0.95         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       96.92        50.40         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        40.77        80.88        51.19 
TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       61.02        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         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R 
       17.33        80.65       194.79         3.68        27.65        12.43 
TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       17.95        11.21        68.12        13.41        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
        5.49         2.04        88.24        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 
       11.97        29.10        11.41        34.29        27.78        20.25 
TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       15.48        87.22        52.27        16.01        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        47.44        33.04        28.80        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK 
       16.31        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       14.83        21.93        38.86        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       12.99        15.91        18.64        15.62        25.28         6.02 

$`7P GAIN WILD-TYPE`
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       59.01        67.30        75.42        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       38.99        24.33        31.20        11.57        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8518 
        0.10        35.18         0.23        29.46        23.28        19.73 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 
       12.46         8.28        12.99         9.63        58.45        25.08 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 
       19.56         7.33        16.87        16.77        10.09        34.49 
TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
       20.61         2.10         6.81         0.16        14.86        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-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
       21.63        40.83        30.28        26.04        13.25         7.66 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 
       11.97         7.92        93.34        44.84        61.28        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 
       26.27        20.12        11.28        13.78        79.86        54.90 
TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
       19.00        10.68         0.43        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC 
       25.15        13.68        16.90        12.92         1.05         0.89 
TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W 
        4.60        73.25        16.80        19.99        85.78        67.17 
TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 
       22.26         0.13        30.38        27.65         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       25.97        21.44        99.78        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SO 
       92.58        50.60        78.90        12.85        27.06        38.63 
TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C 
       18.02         0.53        86.27        52.11        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       18.64        18.05         6.74        13.28 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.13              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           194.79             99.78 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           21.505            21.025 
[1] "0.1 - 194.8 (21.5)" "0.1 - 99.8 (21.0)" 
[1] "hr=" "1.6"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED       112       10        18       10
  7P GAIN WILD-TYPE      55       11        31        4
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I               112                55
  STAGE II               10                11
  STAGE III              18                31
  STAGE IV               10                 4
[1] 4 2
[1] TRUE
[1] "dimension of 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   115  17    25
  7P GAIN WILD-TYPE  61  12    31
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                115                61
  T2                 17                12
  T3+T4              25                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
  7P GAIN MUTATED   21  8  2
  7P GAIN WILD-TYPE 24 14  2
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              21                24
  N1               8                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"
D13V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   49  6
  7P GAIN WILD-TYPE 41  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     49    6
  7P GAIN WILD-TYPE   41    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              49                41
  1               6                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    32 129
  7P GAIN WILD-TYPE  40  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     32  129
  7P GAIN WILD-TYPE   40   68
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              32                40
  MALE               129                68
[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     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          30   115
  7P GAIN WILD-TYPE                        30    72
D13V11, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                 2
  BLACK OR AFRICAN AMERICAN                     30                30
  WHITE                                        115                72
[1] 4 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     6 136
  7P GAIN WILD-TYPE   6  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6  136
  7P GAIN WILD-TYPE    6   84
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 6
  NOT HISPANIC OR LATINO             136                84
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   136  15
  7Q GAIN WILD-TYPE  86  19
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              151               105 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               15                19 
$`7Q GAIN MUTATED`
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-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       34.85        56.81        26.43        30.71        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7288 
        5.29        16.18        22.49         0.13        12.82        61.05 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
       19.13         0.89        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-3468 TCGA-AL-3471 TCGA-AL-3472 
       16.31        15.75        12.46        76.64        13.55        30.35 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61        49.25         2.20        21.67        24.56         3.55 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 
        0.46         6.58        33.83        30.58        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.18        26.40         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 
       43.99        22.06        19.23        17.49        47.80        26.04 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
       25.35        10.88         0.95        11.97         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       48.26        96.92        50.40         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
       24.46         3.75        14.63         3.02        40.77        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       51.19        61.02        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         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       17.98        17.33        80.65       194.79         3.68        27.65 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
       12.43        17.95        11.21        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T TCGA-IZ-8196 TCGA-IZ-A6M8 
       56.75         5.49         2.04        88.24        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 
       20.25        15.48        87.22        52.27        16.01        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
       14.07        47.90        47.44        33.04        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        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV 
       60.03        14.83        21.93        38.86        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY 
       27.39        12.99        15.91        18.64        15.62        25.28 
TCGA-Y8-A8S0 
        6.02 

$`7Q GAIN WILD-TYPE`
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       59.01        67.30        75.42        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       38.99        24.33        31.20        11.57        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8518 
        0.10        35.18         0.23        29.46        23.28        19.73 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 
       12.46         8.28        12.99         9.63        58.45        25.08 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 
       19.56         7.33        16.87        16.77        10.09        34.49 
TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
       20.61         2.10         6.81         0.16        14.86        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-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
       21.63        40.83        30.28        26.04        13.25         7.66 
TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
        7.92        93.34        44.84        61.28        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 
       20.12        11.28        13.78        79.86        54.90        19.00 
TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
       10.68         0.43        48.62        11.05        34.82        25.15 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE 
       13.68        16.90        12.92         1.05         0.89         4.60 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W TCGA-IZ-8195 
       73.25        16.80        19.99        85.78        67.17        22.26 
TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
        0.13        30.38        27.65         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       21.44        99.78        42.94         6.61        84.95        92.58 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SO TCGA-UN-AAZ9 
       50.60        78.90        12.85        27.06        38.63        18.02 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
        0.53        86.27        52.11        26.01        29.00        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       18.05         6.74        13.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.13              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           194.79             99.78 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            21.34             21.44 
[1] "0.1 - 194.8 (21.3)" "0.1 - 99.8 (21.4)" 
[1] "hr=" "1.7"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED       113       10        18       10
  7Q GAIN WILD-TYPE      54       11        31        4
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I               113                54
  STAGE II               10                11
  STAGE III              18                31
  STAGE IV               10                 4
[1] 4 2
[1] TRUE
[1] "dimension of 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   116  17    25
  7Q GAIN WILD-TYPE  60  12    31
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                116                60
  T2                 17                12
  T3+T4              25                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
  7Q GAIN MUTATED   22  8  2
  7Q GAIN WILD-TYPE 23 14  2
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              22                23
  N1               8                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"
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   50  6
  7Q GAIN WILD-TYPE 40  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     50    6
  7Q GAIN WILD-TYPE   40    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              50                40
  1               6                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    32 130
  7Q GAIN WILD-TYPE  40  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     32  130
  7Q GAIN WILD-TYPE   40   67
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              32                40
  MALE               130                67
[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     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          30   116
  7Q GAIN WILD-TYPE                        30    71
D14V11, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                 2
  BLACK OR AFRICAN AMERICAN                     30                30
  WHITE                                        116                71
[1] 4 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     6 137
  7Q GAIN WILD-TYPE   6  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6  137
  7Q GAIN WILD-TYPE    6   83
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 6
  NOT HISPANIC OR LATINO             137                83
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    14   4
  8P GAIN WILD-TYPE 208  30
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18               238 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                30 
$`8P GAIN MUTATED`
TCGA-2Z-A9J2 TCGA-2Z-A9JP TCGA-4A-A93X TCGA-A4-8630 TCGA-AL-3471 TCGA-B1-A47O 
       59.01        29.36        12.82        14.33        13.55        16.87 
TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-7056 TCGA-G7-6789 TCGA-GL-7966 
        0.16        43.20        25.35        20.12         4.01         3.68 
TCGA-GL-A4EM TCGA-IZ-8195 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-SX-A71U TCGA-SX-A7SR 
        1.05        22.26         6.61        16.01        33.04        26.47 

$`8P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         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-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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
       12.99        12.46         9.63        58.45        76.64        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
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-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        26.04        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        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 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
      194.79        12.92        27.65        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       88.24        67.17        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       52.27        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        47.44        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       38.63        16.31        41.62        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        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 
            16.44             21.65 
[1] "0.2 - 59.0 (16.4)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "3"  
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         8        2         5        1
  8P GAIN WILD-TYPE     159       19        44       13
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 8               159
  STAGE II                2                19
  STAGE III               5                44
  STAGE IV                1                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   2     6
  8P GAIN WILD-TYPE 168  27    50
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  8               168
  T2                  2                27
  T3+T4               6                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
  8P GAIN MUTATED    3  3  1
  8P GAIN WILD-TYPE 42 19  3
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0               3                42
  N1               3                19
  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"
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    6  0
  8P GAIN WILD-TYPE 84  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      6    0
  8P GAIN WILD-TYPE   84    9
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               6                84
  1               0                 9
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     7  11
  8P GAIN WILD-TYPE  65 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      7   11
  8P GAIN WILD-TYPE   65  186
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               7                65
  MALE                11               186
[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                49 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7963        TCGA-F9-A97G 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A7SL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-UZ-A9PR        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" 
       TCGA-Y8-A8RZ 
"8P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           0    18
  8P GAIN WILD-TYPE                        60   169
D15V11, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                60
  WHITE                                         18               169
[1] 4 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  15
  8P GAIN WILD-TYPE  11 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   15
  8P GAIN WILD-TYPE   11  205
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              15               205
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    16   7
  8Q GAIN WILD-TYPE 206  27
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23               233 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                27 
$`8Q GAIN MUTATED`
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9JP TCGA-4A-A93X TCGA-A4-8630 TCGA-AL-3466 
       59.01        58.22        29.36        12.82        14.33         9.63 
TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-7056 TCGA-F9-A8NY 
       13.55         0.16        43.20        25.35        20.12         1.18 
TCGA-G7-6789 TCGA-G7-6793 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y TCGA-IZ-8195 
        4.01        11.05         3.68         1.05         2.04        22.26 
TCGA-P4-A5EA TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71U TCGA-SX-A7SR 
        6.61        16.01        14.07        33.04        26.47 

$`8Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
        7.04        75.55       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ 
       38.99        26.43        30.71        24.33        31.20        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 
        5.29        16.18        22.49         0.13        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
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-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        58.45        76.64        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
       43.99        22.06         2.10        19.23         6.81        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-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       44.84        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       13.08         2.40         0.43        51.78        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.33        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 
       19.99        85.78        88.24        67.17        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       84.95        92.58        52.27        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       17.75        47.90        47.44        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        38.63        16.31        41.62        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         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 
            14.07             21.93 
[1] "0.2 - 59.0 (14.1)"  "0.1 - 194.8 (21.9)"
[1] "hr=" "4.7"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         7        3         7        4
  8Q GAIN WILD-TYPE     160       18        42       10
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 7               160
  STAGE II                3                18
  STAGE III               7                42
  STAGE IV                4                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   3    11
  8Q GAIN WILD-TYPE 169  26    45
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  7               169
  T2                  3                26
  T3+T4              11                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
  8Q GAIN MUTATED    2  6  2
  8Q GAIN WILD-TYPE 43 16  2
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0               2                43
  N1               6                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"
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6  2
  8Q GAIN WILD-TYPE 84  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    2
  8Q GAIN WILD-TYPE   84    7
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               6                84
  1               2                 7
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    10  13
  8Q GAIN WILD-TYPE  62 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10   13
  8Q GAIN WILD-TYPE   62  184
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              10                62
  MALE                13               184
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           1    21
  8Q GAIN WILD-TYPE                        59   166
D16V11, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      1                59
  WHITE                                         21               166
[1] 4 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  20
  8Q GAIN WILD-TYPE  11 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   20
  8Q GAIN WILD-TYPE   11  200
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              20               200
[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 220  33
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               253 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                33 
$`9P GAIN MUTATED`
TCGA-B3-4104 TCGA-BQ-7058 TCGA-GL-7966 
       34.49        11.28         3.68 

$`9P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        10.09        30.58        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        20.12         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        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        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.33        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       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 
            11.28             21.44 
[1] "3.7 - 34.5 (11.3)"  "0.1 - 194.8 (21.4)"
[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     167       20        47       14
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0               167
  STAGE II                1                20
  STAGE III               2                47
  STAGE IV                0                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
  9P GAIN MUTATED     0   1     2
  9P GAIN WILD-TYPE 176  28    54
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1                  0               176
  T2                  1                28
  T3+T4               2                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
  9P GAIN MUTATED    0  1  1
  9P GAIN WILD-TYPE 45 21  3
D17V5, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                69 
       TCGA-2Z-A9J1        TCGA-2Z-A9JO        TCGA-4A-A93W        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-A5Y1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A4-A7UZ        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-A47O        TCGA-B1-A655 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B1-A656        TCGA-B1-A657        TCGA-B9-7268        TCGA-BQ-5877 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888        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-5892        TCGA-BQ-5893 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7056        TCGA-DW-7963        TCGA-DZ-6131 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F9-A8NY        TCGA-F9-A97G        TCGA-G7-6789        TCGA-G7-6793 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LD        TCGA-GL-6846 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GL-A59R        TCGA-GL-A9DC        TCGA-IA-A40U        TCGA-IA-A40Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IA-A83W        TCGA-J7-6720        TCGA-J7-8537        TCGA-KV-A74V 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-A5E8        TCGA-P4-A5EA        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" 
       TCGA-Y8-A8RZ 
"9P GAIN WILD-TYPE" 
D17V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  0
  9P GAIN WILD-TYPE 88  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    0
  9P GAIN WILD-TYPE   88    9
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               2                88
  1               0                 9
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1   2
  9P GAIN WILD-TYPE  71 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    2
  9P GAIN WILD-TYPE   71  195
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               1                71
  MALE                 2               195
[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     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0     3
  9P GAIN WILD-TYPE                        60   184
D17V11, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                60
  WHITE                                          3               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"
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0   3
  9P GAIN WILD-TYPE  12 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    3
  9P GAIN WILD-TYPE   12  217
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               3               217
[1] 2 2
[1] FALSE

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     6   1
  10P GAIN WILD-TYPE 216  33
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 7                249 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 33 
$`10P GAIN MUTATED`
TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 TCGA-BQ-5882 TCGA-F9-A7Q0 TCGA-F9-A8NY 
       29.46        76.64         1.15        21.63        13.08         1.18 
TCGA-SX-A7SS 
       48.30 

$`10P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       58.45        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         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-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       10.68         2.40         0.43         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
        6.38        17.98        17.33        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       16.31        41.62        26.47        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        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 
             21.63              21.34 
[1] "1.1 - 76.6 (21.6)"  "0.1 - 194.8 (21.3)"
[1] "hr=" "1.2"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         3        1         2        1
  10P GAIN WILD-TYPE     164       20        47       13
D18V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  3                164
  STAGE II                 1                 20
  STAGE III                2                 47
  STAGE IV                 1                 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 GAIN MUTATED     4   1     3
  10P GAIN WILD-TYPE 172  28    53
D18V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                   4                172
  T2                   1                 28
  T3+T4                3                 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
  10P GAIN MUTATED    2  1  0
  10P GAIN WILD-TYPE 43 21  4
D18V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                2                 43
  N1                1                 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"
D18V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    6  1
  10P GAIN WILD-TYPE 84  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    1
  10P GAIN WILD-TYPE   84    8
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                6                 84
  1                1                  8
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3   5
  10P GAIN WILD-TYPE  69 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    5
  10P GAIN WILD-TYPE   69  192
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                 69
  MALE                  5                192
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 59 
        TCGA-2Z-A9JK         TCGA-4A-A93X         TCGA-4A-A93Y 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LC 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-IA-A40U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SU 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D18V9, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 64 
        TCGA-2Z-A9J2         TCGA-2Z-A9J5         TCGA-2Z-A9J7 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         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-2Z-A9JQ         TCGA-4A-A93W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-8310         TCGA-A4-A48D 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-7268 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-B9-A69E         TCGA-DW-5561 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7963         TCGA-F9-A97G 
"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-A59T 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IZ-A6M8         TCGA-MH-A854         TCGA-MH-A856 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-PJ-A5Z9 
"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-A9PO         TCGA-UZ-A9PR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"10P GAIN WILD-TYPE" 
D18V10, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 50 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         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-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         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-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"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-A9PO         TCGA-UZ-A9PR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"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     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2     2
  10P GAIN WILD-TYPE                        58   185
D18V11, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       2                 58
  WHITE                                           2                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"
D18V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0   6
  10P GAIN WILD-TYPE  12 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    6
  10P GAIN WILD-TYPE   12  214
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                6                214
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     6   1
  10Q GAIN WILD-TYPE 216  33
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                249 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 33 
$`10Q GAIN MUTATED`
TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 TCGA-BQ-5882 TCGA-F9-A7Q0 TCGA-F9-A8NY 
       29.46        76.64         1.15        21.63        13.08         1.18 
TCGA-SX-A7SS 
       48.30 

$`10Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       58.45        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         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-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       10.68         2.40         0.43         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
        6.38        17.98        17.33        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       16.31        41.62        26.47        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        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 
             21.63              21.34 
[1] "1.1 - 76.6 (21.6)"  "0.1 - 194.8 (21.3)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         3        1         2        1
  10Q GAIN WILD-TYPE     164       20        47       13
D19V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  3                164
  STAGE II                 1                 20
  STAGE III                2                 47
  STAGE IV                 1                 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 GAIN MUTATED     4   1     3
  10Q GAIN WILD-TYPE 172  28    53
D19V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                   4                172
  T2                   1                 28
  T3+T4                3                 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
  10Q GAIN MUTATED    2  1  0
  10Q GAIN WILD-TYPE 43 21  4
D19V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                2                 43
  N1                1                 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"
D19V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    6  1
  10Q GAIN WILD-TYPE 84  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    1
  10Q GAIN WILD-TYPE   84    8
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                6                 84
  1                1                  8
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   5
  10Q GAIN WILD-TYPE  69 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    5
  10Q GAIN WILD-TYPE   69  192
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                3                 69
  MALE                  5                192
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 59 
        TCGA-2Z-A9JK         TCGA-4A-A93X         TCGA-4A-A93Y 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-IA-A40U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D19V9, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 64 
        TCGA-2Z-A9J2         TCGA-2Z-A9J5         TCGA-2Z-A9J7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         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-2Z-A9JQ         TCGA-4A-A93W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-8310         TCGA-A4-A48D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-7268 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-B9-A69E         TCGA-DW-5561 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7963         TCGA-F9-A97G 
"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-A59T 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M8         TCGA-MH-A854         TCGA-MH-A856 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-PJ-A5Z9 
"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-A9PO         TCGA-UZ-A9PR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"10Q GAIN WILD-TYPE" 
D19V10, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 50 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         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-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         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-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"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-A9PO         TCGA-UZ-A9PR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"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     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           2     2
  10Q GAIN WILD-TYPE                        58   185
D19V11, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       2                 58
  WHITE                                           2                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"
D19V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   6
  10Q GAIN WILD-TYPE  12 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    6
  10Q GAIN WILD-TYPE   12  214
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                6                214
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     6   4
  11P GAIN WILD-TYPE 216  30
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                246 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 30 
$`11P GAIN MUTATED`
TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B9-4117 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-F9-A7Q0 
        8.48        49.25         0.46        10.88        11.97        13.08 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-P4-A5EA TCGA-P4-A5EB 
       17.33         3.68         6.61        84.95 

$`11P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        25.35        13.25         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        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        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK 
       15.48        99.78        87.22        42.94        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.46               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             84.95             194.79 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            11.425             21.800 
[1] "0.5 - 85.0 (11.4)"  "0.1 - 194.8 (21.8)"
[1] "hr=" "5.2"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         4        0         4        2
  11P GAIN WILD-TYPE     163       21        45       12
D20V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  4                163
  STAGE II                 0                 21
  STAGE III                4                 45
  STAGE IV                 2                 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 GAIN MUTATED     4   2     5
  11P GAIN WILD-TYPE 172  27    51
D20V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                   4                172
  T2                   2                 27
  T3+T4                5                 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
  11P GAIN MUTATED    2  4  0
  11P GAIN WILD-TYPE 43 18  4
D20V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                2                 43
  N1                4                 18
  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 88  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    2
  11P GAIN WILD-TYPE   88    7
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                2                 88
  1                2                  7
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5   6
  11P GAIN WILD-TYPE  67 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    6
  11P GAIN WILD-TYPE   67  191
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                5                 67
  MALE                  6                191
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 58 
        TCGA-2Z-A9JK         TCGA-4A-A93X         TCGA-4A-A93Y 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A5DU 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-A5XZ         TCGA-A4-A6HP         TCGA-AL-3466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-EV-5901 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6790 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-J7-8537         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SO         TCGA-SX-A7SP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SU 
"11P GAIN WILD-TYPE" 
D20V9, continuous
D20V10, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 49 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         TCGA-2Z-A9JN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A5Y0         TCGA-AL-3472 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-A69E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7963         TCGA-F9-A97G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-IA-A40U         TCGA-MH-A854 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E6         TCGA-P4-AAVK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"11P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     1
  11P GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           1     9
  11P GAIN WILD-TYPE                        59   178
D20V11, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       1                 59
  WHITE                                           9                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"
D20V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  11
  11P GAIN WILD-TYPE  12 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   11
  11P GAIN WILD-TYPE   12  209
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               11                209
[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 215  31
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                246 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 31 
$`11Q GAIN MUTATED`
TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B9-4117 TCGA-BQ-5892 TCGA-F9-A7Q0 TCGA-G7-A8LC 
        8.48        49.25         0.46        11.97        13.08        17.33 
TCGA-GL-7966 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-Q2-A5QZ 
        3.68         6.61        84.95        14.07 

$`11Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       10.68         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 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED 
       21.44        15.48        99.78        87.22        42.94        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.46               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             84.95             194.79 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            12.525             21.800 
[1] "0.5 - 85.0 (12.5)"  "0.1 - 194.8 (21.8)"
[1] "hr=" "3.7"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         4        0         4        1
  11Q GAIN WILD-TYPE     163       21        45       13
D21V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  4                163
  STAGE II                 0                 21
  STAGE III                4                 45
  STAGE IV                 1                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  11Q GAIN MUTATED     4   2     4
  11Q GAIN WILD-TYPE 172  27    52
D21V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   4                172
  T2                   2                 27
  T3+T4                4                 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
  11Q GAIN MUTATED    2  2  0
  11Q GAIN WILD-TYPE 43 20  4
D21V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                2                 43
  N1                2                 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"
D21V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  1
  11Q GAIN WILD-TYPE 88  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    1
  11Q GAIN WILD-TYPE   88    8
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                2                 88
  1                1                  8
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     6   4
  11Q GAIN WILD-TYPE  66 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    4
  11Q GAIN WILD-TYPE   66  193
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                6                 66
  MALE                  4                193
[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     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           2     7
  11Q GAIN WILD-TYPE                        58   180
D21V11, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       2                 58
  WHITE                                           7                180
[1] 4 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  12 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   10
  11Q GAIN WILD-TYPE   12  210
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               10                210
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    87  12
  12P GAIN WILD-TYPE 135  22
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                99                157 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                12                 22 
$`12P GAIN MUTATED`
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-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JT TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7997 
       26.43        30.71        22.49        18.21        19.13        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A4ZT 
       29.46        25.64         0.76        19.63        19.73        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 
       16.31        15.75        12.46        76.64        13.55        44.61 
TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       24.56         0.46        33.83        10.16        50.50        28.18 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH 
        1.15        43.99        22.06        19.23         0.16        17.49 
TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 
        8.88        43.20        25.35        10.88         0.95        11.97 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 
        7.63         7.17         3.81        13.61        37.55         3.75 
TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-F9-A7Q0 
       14.63        40.77        80.88        51.19        61.02        13.08 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
        1.18         4.01        39.25         6.38        17.98        17.33 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       16.90       194.79         3.68         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
        0.89        11.21        68.12        11.84        56.75         5.49 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-KV-A6GD 
       16.80         2.04        85.78        88.24        67.17        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 
       29.10        11.41        34.29        27.78        30.38        20.25 
TCGA-MH-A854 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        0.36        84.95        52.27        16.01        12.85        17.75 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       33.04        28.80        11.93        41.62        26.47        48.30 
TCGA-UZ-A9PP TCGA-UZ-A9PX TCGA-Y8-A8RY 
        0.53        27.39        25.28 

$`12P GAIN WILD-TYPE`
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       58.22         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        35.67        38.99        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       25.58         5.29        16.18         0.13        12.82        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05         0.10        35.18         0.89         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-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.48         8.28        12.99         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       25.08        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4103 
       16.87         3.55        16.77         6.58        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
       34.49        12.46        26.40        20.61         0.46        15.12 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        2.10         6.81        14.86        12.30        86.76        19.27 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        26.04        13.25         7.66         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7060 
       50.40        49.84        26.27        20.12        11.28         7.04 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 
       11.61       129.86        35.93        24.46        13.78         3.02 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       79.86        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
        2.40         0.43        51.78        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 
       25.15        13.68        25.84        80.65        12.92        27.65 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        4.60        13.41        73.25        19.99        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A561 TCGA-MH-A855 TCGA-MH-A856 
       16.34        12.36         0.13        27.65        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        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        47.44 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SU TCGA-UN-AAZ9 
       27.06        19.00        38.63        16.31        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        25.68        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.91        18.64        18.05        15.62         6.74         6.02 
TCGA-Y8-A8S1 
       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 
             19.23              21.93 
[1] "0.2 - 194.8 (19.2)" "0.1 - 129.9 (21.9)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED        69        9        13        8
  12P GAIN WILD-TYPE      98       12        36        6
D22V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                 69                 98
  STAGE II                 9                 12
  STAGE III               13                 36
  STAGE IV                 8                  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
  12P GAIN MUTATED    72  10    21
  12P GAIN WILD-TYPE 104  19    35
D22V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                  72                104
  T2                  10                 19
  T3+T4               21                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  12P GAIN MUTATED   15 10  2
  12P GAIN WILD-TYPE 30 12  2
D22V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               15                 30
  N1               10                 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"
D22V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   30  4
  12P GAIN WILD-TYPE 60  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     30    4
  12P GAIN WILD-TYPE   60    5
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               30                 60
  1                4                  5
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    19  88
  12P GAIN WILD-TYPE  53 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     19   88
  12P GAIN WILD-TYPE   53  109
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               19                 53
  MALE                 88                109
[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     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          23    75
  12P GAIN WILD-TYPE                        37   112
D22V11, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                      23                 37
  WHITE                                          75                112
[1] 4 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  92
  12P GAIN WILD-TYPE   9 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   92
  12P GAIN WILD-TYPE    9  128
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               92                128
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    87  12
  12Q GAIN WILD-TYPE 135  22
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                99                157 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                12                 22 
$`12Q GAIN MUTATED`
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-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JT TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7997 
       26.43        30.71        22.49        18.21        19.13        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A4ZT 
       29.46        25.64         0.76        19.63        19.73        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 
       16.31        15.75        12.46        76.64        13.55        44.61 
TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       24.56         0.46        33.83        10.16        50.50        28.18 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH 
        1.15        43.99        22.06        19.23         0.16        17.49 
TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 
        8.88        43.20        25.35        10.88         0.95        11.97 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 
        7.63         7.17         3.81        13.61        37.55         3.75 
TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-F9-A7Q0 
       14.63        40.77        80.88        51.19        61.02        13.08 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
        1.18         4.01        39.25         6.38        17.98        17.33 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       16.90       194.79         3.68         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
        0.89        11.21        68.12        11.84        56.75         5.49 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-KV-A6GD 
       16.80         2.04        85.78        88.24        67.17        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 
       29.10        11.41        34.29        27.78        30.38        20.25 
TCGA-MH-A854 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        0.36        84.95        52.27        16.01        12.85        17.75 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       33.04        28.80        11.93        41.62        26.47        48.30 
TCGA-UZ-A9PP TCGA-UZ-A9PX TCGA-Y8-A8RY 
        0.53        27.39        25.28 

$`12Q GAIN WILD-TYPE`
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       58.22         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        35.67        38.99        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       25.58         5.29        16.18         0.13        12.82        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05         0.10        35.18         0.89         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-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.48         8.28        12.99         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       25.08        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4103 
       16.87         3.55        16.77         6.58        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
       34.49        12.46        26.40        20.61         0.46        15.12 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        2.10         6.81        14.86        12.30        86.76        19.27 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        26.04        13.25         7.66         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7060 
       50.40        49.84        26.27        20.12        11.28         7.04 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 
       11.61       129.86        35.93        24.46        13.78         3.02 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       79.86        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
        2.40         0.43        51.78        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 
       25.15        13.68        25.84        80.65        12.92        27.65 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        4.60        13.41        73.25        19.99        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A561 TCGA-MH-A855 TCGA-MH-A856 
       16.34        12.36         0.13        27.65        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        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        47.44 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SU TCGA-UN-AAZ9 
       27.06        19.00        38.63        16.31        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        25.68        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.91        18.64        18.05        15.62         6.74         6.02 
TCGA-Y8-A8S1 
       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 
             19.23              21.93 
[1] "0.2 - 194.8 (19.2)" "0.1 - 129.9 (21.9)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED        69        9        13        8
  12Q GAIN WILD-TYPE      98       12        36        6
D23V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                 69                 98
  STAGE II                 9                 12
  STAGE III               13                 36
  STAGE IV                 8                  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
  12Q GAIN MUTATED    72  10    21
  12Q GAIN WILD-TYPE 104  19    35
D23V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                  72                104
  T2                  10                 19
  T3+T4               21                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  12Q GAIN MUTATED   15 10  2
  12Q GAIN WILD-TYPE 30 12  2
D23V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               15                 30
  N1               10                 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"
D23V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   30  4
  12Q GAIN WILD-TYPE 60  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     30    4
  12Q GAIN WILD-TYPE   60    5
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               30                 60
  1                4                  5
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    19  88
  12Q GAIN WILD-TYPE  53 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     19   88
  12Q GAIN WILD-TYPE   53  109
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               19                 53
  MALE                 88                109
[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     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          23    75
  12Q GAIN WILD-TYPE                        37   112
D23V11, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                      23                 37
  WHITE                                          75                112
[1] 4 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  92
  12Q GAIN WILD-TYPE   9 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   92
  12Q GAIN WILD-TYPE    9  128
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               92                128
[1] 2 2
[1] FALSE

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    22   3
  13Q GAIN WILD-TYPE 200  31
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                25                231 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 31 
$`13Q GAIN MUTATED`
TCGA-2Z-A9J1 TCGA-4A-A93X TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A5Y1 
       75.55        12.82        23.97        19.73        14.33        12.99 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-5885 
        2.20        19.56        12.46         0.46         1.15        30.28 
TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6796 
       96.92        13.61        51.19        24.89        51.78        34.82 
TCGA-MH-A856 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-UZ-A9PX 
       25.97         6.61        84.95        19.00        41.62        27.39 
TCGA-Y8-A897 
       18.05 

$`13Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A48D 
       25.64        23.28        23.31         0.76        19.63        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-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       44.61        49.25         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        26.04        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.17         3.81        11.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        61.02        54.90        34.19        19.00 
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-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        39.25        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
        6.38        17.98        17.33        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED 
       21.44        15.48        99.78        87.22        42.94        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       11.93        38.63        16.31        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       38.86        52.11        30.67        25.68        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        15.91        18.64        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.46               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             96.92             194.79 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             19.73              21.44 
[1] "0.5 - 96.9 (19.7)"  "0.1 - 194.8 (21.4)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED        18        0         5        0
  13Q GAIN WILD-TYPE     149       21        44       14
D24V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                 18                149
  STAGE II                 0                 21
  STAGE III                5                 44
  STAGE IV                 0                 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    20   1     4
  13Q GAIN WILD-TYPE 156  28    52
D24V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                  20                156
  T2                   1                 28
  T3+T4                4                 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
  13Q GAIN MUTATED    5  2  0
  13Q GAIN WILD-TYPE 40 20  4
D24V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                5                 40
  N1                2                 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"
D24V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   10  0
  13Q GAIN WILD-TYPE 80  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     10    0
  13Q GAIN WILD-TYPE   80    9
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               10                 80
  1                0                  9
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     7  19
  13Q GAIN WILD-TYPE  65 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7   19
  13Q GAIN WILD-TYPE   65  178
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                7                 65
  MALE                 19                178
[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     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           4    21
  13Q GAIN WILD-TYPE                        56   166
D24V11, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       4                 56
  WHITE                                          21                166
[1] 4 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  21
  13Q GAIN WILD-TYPE  10 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   21
  13Q GAIN WILD-TYPE   10  199
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               21                199
[1] 2 2
[1] FALSE

Clustering(25) Variable = 14Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     1   1
  14Q GAIN WILD-TYPE 221  33
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                254 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 33 
$`14Q GAIN MUTATED`
TCGA-BQ-5880 TCGA-GL-7966 
       43.20         3.68 

$`14Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
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-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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
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        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.68               0.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             43.20             194.79 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             23.44              21.39 
[1] "3.7 - 43.2 (23.4)"  "0.1 - 194.8 (21.4)"
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
D25V2, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                262 
        TCGA-2K-A9WE         TCGA-2Z-A9J1         TCGA-2Z-A9J2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J5         TCGA-2Z-A9J6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9J9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JE         TCGA-2Z-A9JG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JJ         TCGA-2Z-A9JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JL         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-A9JQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JR         TCGA-2Z-A9JS         TCGA-2Z-A9JT 
"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-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         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-A5Y1         TCGA-A4-A6HP         TCGA-A4-A772 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A7UZ         TCGA-AL-3466         TCGA-AL-3467 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3468         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-AL-A5DJ 
"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-A47M         TCGA-B1-A47N         TCGA-B1-A47O 
"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-B1-A657         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-B3-A6W5         TCGA-B9-4113         TCGA-B9-4114 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A5W8         TCGA-B9-A5W9         TCGA-B9-A69E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A8YH         TCGA-B9-A8YI         TCGA-BQ-5875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5881         TCGA-BQ-5882 
"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-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"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-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         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-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-DW-7963         TCGA-DZ-6131 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-F9-A4JJ         TCGA-F9-A7Q0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A7VF         TCGA-F9-A8NY         TCGA-F9-A97G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-6846 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-8500         TCGA-GL-A4EM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A59T         TCGA-GL-A9DC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-GL-A9DE         TCGA-HE-A5NF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HE-A5NH         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-HE-A5NL         TCGA-IA-A40U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-IA-A83S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A83T         TCGA-IA-A83W         TCGA-IZ-8195 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-8196         TCGA-IZ-A6M8         TCGA-IZ-A6M9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-KV-A6GD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KV-A6GE         TCGA-KV-A74V         TCGA-MH-A55W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A55Z         TCGA-MH-A560         TCGA-MH-A561 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A562         TCGA-MH-A854         TCGA-MH-A855 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-MH-A857         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-PJ-A5Z8         TCGA-PJ-A5Z9 
"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-A7SL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"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-A9PO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PP         TCGA-UZ-A9PQ         TCGA-UZ-A9PR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PU         TCGA-UZ-A9PV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-UZ-A9PZ         TCGA-UZ-A9Q0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9Q1         TCGA-Y8-A894         TCGA-Y8-A895 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A897         TCGA-Y8-A898 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ         TCGA-Y8-A8S0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8S1 
"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     167       21        46       14
D25V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  0                167
  STAGE II                 0                 21
  STAGE III                3                 46
  STAGE IV                 0                 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
  14Q GAIN MUTATED     0   0     3
  14Q GAIN WILD-TYPE 176  29    53
D25V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                   0                176
  T2                   0                 29
  T3+T4                3                 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
  14Q GAIN MUTATED    0  2  0
  14Q GAIN WILD-TYPE 45 20  4
D25V5, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 69 
        TCGA-2Z-A9J1         TCGA-2Z-A9JO         TCGA-4A-A93W 
"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-A5Y1         TCGA-A4-A7UZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-3473 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-A47O 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B1-A657 
"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-5888         TCGA-BQ-5889 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-F9-A97G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6793         TCGA-G7-6795 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LD         TCGA-GL-6846 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A9DC         TCGA-IA-A40U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83W         TCGA-J7-6720 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-J7-8537         TCGA-KV-A74V         TCGA-P4-A5E6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-SX-A71R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SP         TCGA-SX-A7SS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UN-AAZ9         TCGA-UZ-A9PM         TCGA-UZ-A9PQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-Y8-A897         TCGA-Y8-A8RZ 
"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 88  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    0
  14Q GAIN WILD-TYPE   88    9
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                2                 88
  1                0                  9
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE  70 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    1
  14Q GAIN WILD-TYPE   70  196
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                 70
  MALE                  1                196
[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     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           0     2
  14Q GAIN WILD-TYPE                        60   185
D25V11, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                252 
        TCGA-2K-A9WE         TCGA-2Z-A9J1         TCGA-2Z-A9J2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J5         TCGA-2Z-A9J6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9J9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JE         TCGA-2Z-A9JG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JJ         TCGA-2Z-A9JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JL         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-A9JQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JR         TCGA-2Z-A9JS         TCGA-2Z-A9JT 
"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-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         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-A5Y1         TCGA-A4-A6HP         TCGA-A4-A772 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A7UZ         TCGA-AL-3466         TCGA-AL-3467 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3468         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-AL-A5DJ 
"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-A47M         TCGA-B1-A47N         TCGA-B1-A47O 
"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-B1-A657         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-B3-A6W5         TCGA-B9-4113         TCGA-B9-4114 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A5W8         TCGA-B9-A5W9         TCGA-B9-A69E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A8YH         TCGA-B9-A8YI         TCGA-BQ-5875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5881         TCGA-BQ-5883 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-7044         TCGA-BQ-7045 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"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-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6133         TCGA-DZ-6134 
"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-A59T         TCGA-GL-A9DC         TCGA-GL-A9DD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A9DE         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-A83W         TCGA-IZ-8195         TCGA-IZ-8196 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M8         TCGA-IZ-A6M9         TCGA-J7-6720 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-J7-8537         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-A855         TCGA-MH-A856 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A857         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-PJ-A5Z8         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SM         TCGA-SX-A7SN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SO         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-A9PO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PP         TCGA-UZ-A9PQ         TCGA-UZ-A9PR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PU         TCGA-UZ-A9PV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-UZ-A9PZ         TCGA-UZ-A9Q0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-UZ-A9Q1         TCGA-WN-A9G9         TCGA-WN-AB4C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A895         TCGA-Y8-A896 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A897         TCGA-Y8-A898         TCGA-Y8-A8RY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-Y8-A8S0         TCGA-Y8-A8S1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D25V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   1
  14Q GAIN WILD-TYPE  12 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    1
  14Q GAIN WILD-TYPE   12  219
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                1                219
[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 218  33
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                251 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 33 
$`15Q GAIN MUTATED`
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-BQ-5892 TCGA-P4-A5EB TCGA-Q2-A5QZ 
       49.25         7.33        11.97        84.95        14.07 

$`15Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       44.61         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        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        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.22        42.94         6.61        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       16.01        50.60        78.90        12.85        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              7.33               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             84.95             194.79 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             14.07              21.44 
[1] "7.3 - 85.0 (14.1)"  "0.1 - 194.8 (21.4)"
[1] "hr=" "1.4"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         2        1         2        0
  15Q GAIN WILD-TYPE     165       20        47       14
D26V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  2                165
  STAGE II                 1                 20
  STAGE III                2                 47
  STAGE IV                 0                 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
  15Q GAIN MUTATED     2   1     2
  15Q GAIN WILD-TYPE 174  28    54
D26V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                   2                174
  T2                   1                 28
  T3+T4                2                 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
  15Q GAIN MUTATED    1  0  0
  15Q GAIN WILD-TYPE 44 22  4
D26V5, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 70 
        TCGA-2Z-A9J1         TCGA-2Z-A9JO         TCGA-4A-A93W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y1         TCGA-A4-A7UZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-3473 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-A47O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B1-A657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5888 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-F9-A97G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6793         TCGA-G7-6795 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LD         TCGA-GL-6846 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-A59R         TCGA-GL-A9DC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40Y         TCGA-IA-A83W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-KV-A74V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-A5E8         TCGA-P4-A5EA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A7SM         TCGA-SX-A7SP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UN-AAZ9         TCGA-UZ-A9PM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PQ         TCGA-UZ-A9PX         TCGA-Y8-A897 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"15Q GAIN WILD-TYPE" 
D26V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    1  0
  15Q GAIN WILD-TYPE 89  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    0
  15Q GAIN WILD-TYPE   89    9
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                1                 89
  1                0                  9
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3   2
  15Q GAIN WILD-TYPE  69 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    2
  15Q GAIN WILD-TYPE   69  195
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 69
  MALE                  2                195
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 59 
        TCGA-2Z-A9JK         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-A4-8310 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-8630         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-5560         TCGA-DW-5561 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         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-A7SO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU 
"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                 63 
        TCGA-2Z-A9J2         TCGA-2Z-A9J5         TCGA-2Z-A9J7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         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-2Z-A9JQ         TCGA-4A-A93W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-8310         TCGA-A4-A48D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3466 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-7268 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-B9-A69E         TCGA-DW-5561 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7963         TCGA-F9-A97G 
"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-A59T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M8         TCGA-MH-A854         TCGA-MH-A856 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-Y8-A894 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"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                 50 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         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-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         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-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"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-A9PO         TCGA-UZ-A9PR 
"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-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"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     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           2     3
  15Q GAIN WILD-TYPE                        58   184
D26V11, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       2                 58
  WHITE                                           3                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"
D26V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0   5
  15Q GAIN WILD-TYPE  12 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    5
  15Q GAIN WILD-TYPE   12  215
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                5                215
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   119  16
  16P GAIN WILD-TYPE 103  18
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               135                121 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                 18 
$`16P GAIN MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JJ 
        7.04        75.55        58.22       100.27        56.91        35.67 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93X 
       29.36        25.58         5.29        16.18        22.49        12.82 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-7997 
       18.21        61.05         0.10        35.18        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        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-A5Y1 TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-5398 
       12.99         9.63        76.64        13.55         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 
       21.67         6.58        30.58        12.46        10.16        28.18 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         0.16        12.30        86.76        43.20        47.80 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 
       26.04        25.35         7.66         0.95       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7834 
       96.92        50.40        11.28         7.04         3.81       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5902 
       35.93        24.46        40.77        51.19        61.02        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        17.33       194.79         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
       27.65         1.05        17.95         0.89        11.21        68.12 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S 
       11.84        56.75         5.49        16.80         2.04        85.78 
TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       22.26        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A854 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       34.29        30.38         0.36        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 
        6.61        84.95        52.27        50.60        78.90        17.75 
TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       47.90        33.04        28.80        27.06        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP 
       41.62        26.47        48.30        60.03        14.83         0.53 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       52.11        30.67        25.68        27.39        12.99        15.91 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8S0 
       18.05        15.62         6.02 

$`16P GAIN WILD-TYPE`
TCGA-2Z-A9J2 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       59.01         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       54.64        51.52        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7734 
       31.20         0.13        11.57        19.63        19.13         0.89 
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        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47N 
       30.35        25.08        44.61        49.25         7.33        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       16.87         3.55        16.77         0.46        33.83        10.09 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E 
       34.49        50.50        26.40        20.61         6.81        14.86 
TCGA-B9-A8YH TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 
       17.49        19.27         8.88        63.72        22.92        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 
       40.83        26.04        30.28        13.25        10.88        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 
        7.92         2.76        93.34        44.84        61.28        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 
       26.27        20.12         7.63         7.17        11.61        13.61 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
       37.55        13.78         3.75        14.63         3.02        79.86 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6793 
       80.88        54.90        34.19        10.68        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
       39.25        34.82        13.68        25.84         6.38        16.90 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-A59R TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK 
       80.65        12.92        12.43         4.60        13.41        73.25 
TCGA-IA-A40X TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-J7-8537 TCGA-MH-A55Z 
       19.99        88.24        67.17        21.34         0.13        27.78 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       27.65        20.25        12.13        25.97        21.44        15.48 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM 
       92.58        16.01        12.85        14.07        47.44        11.93 
TCGA-SX-A7SO TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       38.63        43.76        18.02        21.93        86.27        38.86 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       26.01        29.00        18.64        18.64        25.28         6.74 
TCGA-Y8-A8S1 
       13.28 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.10               0.13 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            194.79              93.34 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             19.63              21.63 
[1] "0.1 - 194.8 (19.6)" "0.1 - 93.3 (21.6)" 
[1] "hr=" "1.3"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED        88       12        26        6
  16P GAIN WILD-TYPE      79        9        23        8
D27V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                 88                 79
  STAGE II                12                  9
  STAGE III               26                 23
  STAGE IV                 6                  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   94 17    27
  16P GAIN WILD-TYPE 82 12    29
D27V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                  94                 82
  T2                  17                 12
  T3+T4               27                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16P GAIN MUTATED   23 11  2
  16P GAIN WILD-TYPE 22 11  2
D27V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               23                 22
  N1               11                 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   46  3
  16P GAIN WILD-TYPE 44  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     46    3
  16P GAIN WILD-TYPE   44    6
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               46                 44
  1                3                  6
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    27 116
  16P GAIN WILD-TYPE  45  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     27  116
  16P GAIN WILD-TYPE   45   81
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               27                 45
  MALE                116                 81
[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     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          20   111
  16P GAIN WILD-TYPE                        40    76
D27V11, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           3                  2
  BLACK OR AFRICAN AMERICAN                      20                 40
  WHITE                                         111                 76
[1] 4 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     4 120
  16P GAIN WILD-TYPE   8 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4  120
  16P GAIN WILD-TYPE    8  100
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO              120                100
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   118  13
  16Q GAIN WILD-TYPE 104  21
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               131                125 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                 21 
$`16Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JJ 
        7.04        75.55        58.22       100.27        56.91        35.67 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93X 
       29.36        25.58         5.29        16.18        22.49        12.82 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-7997 
       18.21        61.05         0.10        35.18        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        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-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A657 
       76.64        13.55         2.20        19.56        21.67         6.58 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 
       30.58        12.46        10.16        28.18         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 
       15.12        43.99        22.06         2.10        19.23         0.16 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 
       12.30        86.76        43.20        47.80        26.04        25.35 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 
        0.95       123.62        48.26        96.92        50.40         7.04 
TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6133 
        3.81       129.86        35.93        24.46        40.77        51.19 
TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       61.02        19.00        24.89        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC 
        0.43         4.01        51.78        25.15        17.98        17.33 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-GL-A9DC 
      194.79         3.68        27.65         1.05        17.95         0.89 
TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.21        68.12        11.84         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
        2.04        85.78        22.26        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A854 TCGA-P4-A5E6 
       29.10        11.41        34.29        30.38         0.36        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM 
       87.22        42.94         6.61        84.95        52.27        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       78.90        17.75        47.90        33.04        28.80        27.06 
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        48.30        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       14.83         0.53        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8S0 
       12.99        15.91        18.05        15.62         6.02 

$`16Q GAIN WILD-TYPE`
TCGA-2Z-A9J2 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       59.01         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       54.64        51.52        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7734 
       31.20         0.13        11.57        19.63        19.13         0.89 
TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        0.23        29.46        23.28         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        9.63        58.45        30.35        25.08        44.61        49.25 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
        7.33        24.56        16.87         3.55        16.77         0.46 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 
       33.83        10.09        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 
        6.81        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-5888 
       22.92        21.63        40.83        26.04        30.28        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 
       10.88         7.66        11.97         7.92         2.76        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       44.84        61.28        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 
        7.63         7.17        11.61        13.61        37.55        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
        3.75        14.63         3.02        79.86        80.88        54.90 
TCGA-EV-5901 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
       34.19        10.68        48.62        11.05        39.25        34.82 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 
       13.68        25.84         6.38        16.90        80.65        12.92 
TCGA-GL-A59R TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A83T 
       12.43         4.60        13.41        56.75        73.25        88.24 
TCGA-IA-A83W TCGA-IZ-8196 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 
       67.17        21.34         0.13        27.78        27.65        20.25 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5ED TCGA-P4-AAVL 
       12.13        25.97        21.44        15.48        92.58        16.01 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU 
       12.85        14.07        47.44        11.93        38.63        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-WN-A9G9 TCGA-WN-AB4C 
       18.02        21.93        86.27        38.86        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       18.64        18.64        25.28         6.74        13.28 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.10               0.13 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            194.79              93.34 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             19.99              21.44 
[1] "0.1 - 194.8 (20.0)" "0.1 - 93.3 (21.4)" 
[1] "hr=" "1.8"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED        89       12        23        5
  16Q GAIN WILD-TYPE      78        9        26        9
D28V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                 89                 78
  STAGE II                12                  9
  STAGE III               23                 26
  STAGE IV                 5                  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   93 17    24
  16Q GAIN WILD-TYPE 83 12    32
D28V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                  93                 83
  T2                  17                 12
  T3+T4               24                 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
  16Q GAIN MUTATED   22  9  1
  16Q GAIN WILD-TYPE 23 13  3
D28V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               22                 23
  N1                9                 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   43  2
  16Q GAIN WILD-TYPE 47  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     43    2
  16Q GAIN WILD-TYPE   47    7
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               43                 47
  1                2                  7
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    28 111
  16Q GAIN WILD-TYPE  44  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     28  111
  16Q GAIN WILD-TYPE   44   86
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               28                 44
  MALE                111                 86
[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     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          21   107
  16Q GAIN WILD-TYPE                        39    80
D28V11, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           3                  2
  BLACK OR AFRICAN AMERICAN                      21                 39
  WHITE                                         107                 80
[1] 4 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     4 117
  16Q GAIN WILD-TYPE   8 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4  117
  16Q GAIN WILD-TYPE    8  103
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO              117                103
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED   140  15
  17P GAIN WILD-TYPE  82  19
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               155                101 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                15                 19 
$`17P GAIN MUTATED`
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-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ 
        4.57        34.85        56.81        30.71        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-A4-7286 TCGA-A4-7288 
        5.29        16.18        22.49         0.13        18.21        61.05 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
       19.13         0.89        16.64        25.64        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU 
        0.76        19.63        19.73        14.33        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       15.75         8.28        12.46        76.64        13.55        30.35 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       49.25         2.20         7.33        21.67        24.56         3.55 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        6.58        33.83        30.58        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5887 
       22.06        19.23         0.16        17.49        47.80        25.35 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 
        0.95        11.97         7.92        48.26        96.92        50.40 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.04         3.81        11.61        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-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 
       40.77        51.19        61.02        34.19        24.89        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 
        2.40         1.18         4.01        51.78        39.25        34.82 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
      194.79         3.68         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       11.21        68.12        13.41        11.84        56.75         5.49 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80         2.04        88.24        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        15.48        87.22 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        6.61        84.95        16.01        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       47.44        33.04        28.80        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP 
       26.47        48.30        43.76        60.03        14.83         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       29.00        15.91        15.62        25.28         6.02 

$`17P GAIN WILD-TYPE`
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       67.30        75.42        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 
       26.43        24.33        31.20        12.82        11.57        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8312 
        0.10        35.18         0.23        30.48        29.46        23.28 
TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 
       12.46         8.48        12.99         9.63        58.45        25.08 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 
       44.61        19.56        16.87        16.77         0.46        10.09 
TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI 
       34.49        20.61         2.10         6.81        14.86        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-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 
       10.88         7.66         2.76       123.62        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ 
        7.17        79.86        80.88        54.90        19.00        10.68 
TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 
        0.43        48.62        11.05        25.15        13.68        12.92 
TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W 
       27.65         4.60        73.25        19.99        85.78        67.17 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 
        0.36        12.13        25.97        21.44        99.78        42.94 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SL 
       92.58        52.27        50.60        78.90        12.85        27.06 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 
       11.93        38.63        18.02        21.93        86.27        26.01 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       18.64        18.64        18.05         6.74        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 
             19.63              22.92 
[1] "0.1 - 194.8 (19.6)" "0.1 - 123.6 (22.9)"
[1] "hr=" "1.6"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED       117       14        18        6
  17P GAIN WILD-TYPE      50        7        31        8
D29V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                117                 50
  STAGE II                14                  7
  STAGE III               18                 31
  STAGE IV                 6                  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
  17P GAIN MUTATED   120  20    23
  17P GAIN WILD-TYPE  56   9    33
D29V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                 120                 56
  T2                  20                  9
  T3+T4               23                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17P GAIN MUTATED   22  9  1
  17P GAIN WILD-TYPE 23 13  3
D29V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               22                 23
  N1                9                 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"
D29V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   43  3
  17P GAIN WILD-TYPE 47  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     43    3
  17P GAIN WILD-TYPE   47    6
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               43                 47
  1                3                  6
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    36 129
  17P GAIN WILD-TYPE  36  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     36  129
  17P GAIN WILD-TYPE   36   68
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               36                 36
  MALE                129                 68
[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     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          29   122
  17P GAIN WILD-TYPE                        31    65
D29V11, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           4                  1
  BLACK OR AFRICAN AMERICAN                      29                 31
  WHITE                                         122                 65
[1] 4 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     5 145
  17P GAIN WILD-TYPE   7  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5  145
  17P GAIN WILD-TYPE    7   75
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  7
  NOT HISPANIC OR LATINO              145                 75
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   151  19
  17Q GAIN WILD-TYPE  71  15
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               170                 86 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                 15 
$`17Q GAIN MUTATED`
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-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JP 
        4.57        34.85        56.81        51.52        30.71        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-A4-7286 
       25.58         5.29        16.18        22.49         0.13        18.21 
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 
       61.05        19.13         0.89         0.23        16.64        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-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-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-A5DJ TCGA-AT-A5NU 
        9.63        76.64        13.55        30.35        49.25         2.20 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        6.58        33.83        30.58        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 
       22.06         2.10        19.23         0.16        17.49        86.76 
TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
       47.80        26.04        25.35        13.25         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7053 
       11.97         7.92        48.26        96.92        50.40        49.84 
TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       11.28         7.04         3.81        11.61        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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 
        3.02        40.77        80.88        51.19        61.02        34.19 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
       24.89        13.08         2.40         1.18         4.01        51.78 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       11.05        39.25        34.82        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM 
       17.33        16.90        80.65       194.79         3.68         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH 
       12.43        17.95         0.89        11.21        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83T 
       11.84        56.75         5.49        16.80         2.04        88.24 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
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-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVL 
       20.25        15.48        87.22         6.61        84.95        16.01 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        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        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       60.03        14.83         0.53        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A898 
       25.68        27.39        12.99        29.00        15.91        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

$`17Q GAIN WILD-TYPE`
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       67.30        75.42        54.64        35.67        38.99        26.43 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7583 
       24.33        31.20        12.82        11.57        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A48D TCGA-A4-A5Y1 
       35.18        30.48        29.46        23.28        12.46        12.99 
TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-3926 
       58.45        25.08        44.61        19.56         0.46        10.09 
TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 
       34.49        20.61         6.81        14.86        12.30        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-5894 TCGA-BQ-7044 TCGA-BQ-7048 
       26.04        30.28        10.88         2.76       123.62        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 
       44.84        61.28        26.27        20.12         7.63         7.17 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 
       79.86        54.90        19.00        10.68         0.43        48.62 
TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NK 
       25.15        13.68        12.92        27.65         4.60        73.25 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       19.99        85.78        67.17         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM 
       21.44        99.78        42.94        92.58        52.27        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UN-AAZ9 
       78.90        12.85        27.06        11.93        38.63        18.02 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       21.93        86.27        26.01        18.64        18.64        18.05 
TCGA-Y8-A8RZ TCGA-Y8-A8S1 
        6.74        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 
            19.065             24.705 
[1] "0.1 - 194.8 (19.1)" "0.1 - 123.6 (24.7)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED       121       15        25        9
  17Q GAIN WILD-TYPE      46        6        24        5
D30V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                121                 46
  STAGE II                15                  6
  STAGE III               25                 24
  STAGE IV                 9                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  17Q GAIN MUTATED   124  22    32
  17Q GAIN WILD-TYPE  52   7    24
D30V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                 124                 52
  T2                  22                  7
  T3+T4               32                 24
[1] 3 2
[1] 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   28 10  3
  17Q GAIN WILD-TYPE 17 12  1
D30V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               28                 17
  N1               10                 12
  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   50  5
  17Q GAIN WILD-TYPE 40  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     50    5
  17Q GAIN WILD-TYPE   40    4
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               50                 40
  1                5                  4
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    43 137
  17Q GAIN WILD-TYPE  29  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     43  137
  17Q GAIN WILD-TYPE   29   60
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               43                 29
  MALE                137                 60
[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     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          32   133
  17Q GAIN WILD-TYPE                        28    54
D30V11, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           4                  1
  BLACK OR AFRICAN AMERICAN                      32                 28
  WHITE                                         133                 54
[1] 4 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     6 155
  17Q GAIN WILD-TYPE   6  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  155
  17Q GAIN WILD-TYPE    6   65
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  6
  NOT HISPANIC OR LATINO              155                 65
[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 212  32
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                244 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 32 
$`18P GAIN MUTATED`
TCGA-2Z-A9J1 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-5155 
       75.55        12.99         9.63        30.58        34.49        15.12 
TCGA-DW-5560 TCGA-G7-6790 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-HE-A5NJ TCGA-SX-A7SS 
       11.61        51.78        17.98        17.33        56.75        48.30 

$`18P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 
       16.77         0.46         6.58        33.83        10.09        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        43.99        22.06         2.10        19.23         6.81 
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-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.04         7.17         3.81        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
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-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43         4.01        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
       34.82        25.15        13.68        25.84         6.38        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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       13.41        11.84        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        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         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 
       38.63        16.31        41.62        26.47        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         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 
             24.28              21.39 
[1] "9.6 - 75.5 (24.3)"  "0.1 - 194.8 (21.4)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         6        1         2        2
  18P GAIN WILD-TYPE     161       20        47       12
D31V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  6                161
  STAGE II                 1                 20
  STAGE III                2                 47
  STAGE IV                 2                 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
  18P GAIN MUTATED     8   2     2
  18P GAIN WILD-TYPE 168  27    54
D31V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   8                168
  T2                   2                 27
  T3+T4                2                 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
  18P GAIN MUTATED    2  2  0
  18P GAIN WILD-TYPE 43 20  4
D31V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                2                 43
  N1                2                 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"
D31V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    5  1
  18P GAIN WILD-TYPE 85  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    1
  18P GAIN WILD-TYPE   85    8
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                5                 85
  1                1                  8
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1  11
  18P GAIN WILD-TYPE  71 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   11
  18P GAIN WILD-TYPE   71  186
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                 71
  MALE                 11                186
[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                 49 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         TCGA-2Z-A9JN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-7501 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"18P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           0    11
  18P GAIN WILD-TYPE                        60   176
D31V11, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 60
  WHITE                                          11                176
[1] 4 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  12 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   11
  18P GAIN WILD-TYPE   12  209
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               11                209
[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 213  34
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                247 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                 34 
$`18Q GAIN MUTATED`
TCGA-2Z-A9J1 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-5155 TCGA-DW-5560 TCGA-G7-6790 
       75.55        30.58        34.49        15.12        11.61        51.78 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-SX-A7SS 
       17.98        17.33        48.30 

$`18Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       10.09        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       20.61         0.46         1.15        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         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-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 
       11.28         7.63         7.04         7.17         3.81        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 
       13.08         2.40         1.18         0.43         4.01        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
        6.38        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             11.61               0.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             75.55             194.79 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             30.58              21.34 
[1] "11.6 - 75.5 (30.6)" "0.1 - 194.8 (21.3)"
[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     161       20        48       13
D32V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  6                161
  STAGE II                 1                 20
  STAGE III                1                 48
  STAGE IV                 1                 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
  18Q GAIN MUTATED     6   2     1
  18Q GAIN WILD-TYPE 170  27    55
D32V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                   6                170
  T2                   2                 27
  T3+T4                1                 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
  18Q GAIN MUTATED    2  0  0
  18Q GAIN WILD-TYPE 43 22  4
D32V5, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 69 
        TCGA-2Z-A9JO         TCGA-4A-A93W         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-A5Y1         TCGA-A4-A7UZ         TCGA-AL-3466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-A47O         TCGA-B1-A655 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-A656         TCGA-B1-A657         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-5888         TCGA-BQ-5889 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-F9-A97G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6789         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-GL-6846 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-A59R         TCGA-GL-A9DC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40Y         TCGA-IA-A83W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-KV-A74V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-A5E8         TCGA-P4-A5EA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A7SM         TCGA-SX-A7SP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-UN-AAZ9         TCGA-UZ-A9PM         TCGA-UZ-A9PQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-Y8-A897         TCGA-Y8-A8RZ 
"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 86  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE   86    9
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                4                 86
  1                0                  9
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1   8
  18Q GAIN WILD-TYPE  71 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    8
  18Q GAIN WILD-TYPE   71  189
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 71
  MALE                  8                189
[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                 63 
        TCGA-2Z-A9J2         TCGA-2Z-A9J5         TCGA-2Z-A9J7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         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-2Z-A9JQ         TCGA-4A-A93W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-8310         TCGA-A4-A48D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-7268 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-B9-A69E         TCGA-DW-5561 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7963         TCGA-F9-A97G 
"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-A59T         TCGA-GL-A9DD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-Y8-A894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"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                 49 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         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-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         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-IA-A40U 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"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" 
        TCGA-Y8-A8RZ 
"18Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0     9
  18Q GAIN WILD-TYPE                        60   178
D32V11, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 60
  WHITE                                           9                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"
D32V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   9
  18Q GAIN WILD-TYPE  12 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    9
  18Q GAIN WILD-TYPE   12  211
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                9                211
[1] 2 2
[1] FALSE

Clustering(33) Variable = 19P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     4   0
  19P GAIN WILD-TYPE 218  34
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                252 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                 34 
$`19P GAIN MUTATED`
TCGA-BQ-5885 TCGA-BQ-5892 TCGA-G7-A8LC TCGA-GL-7966 
       30.28        11.97        17.33         3.68 

$`19P GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        26.04        25.35        13.25        10.88 
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-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        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        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         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 
            14.650             21.535 
[1] "3.7 - 30.3 (14.6)"  "0.1 - 194.8 (21.5)"
[1] "hr="     "3300000"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         2        0         2        0
  19P GAIN WILD-TYPE     165       21        47       14
D33V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  2                165
  STAGE II                 0                 21
  STAGE III                2                 47
  STAGE IV                 0                 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 GAIN MUTATED     2   0     2
  19P GAIN WILD-TYPE 174  29    54
D33V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                   2                174
  T2                   0                 29
  T3+T4                2                 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
  19P GAIN MUTATED    2  1  0
  19P GAIN WILD-TYPE 43 21  4
D33V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                2                 43
  N1                1                 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"
D33V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  0
  19P GAIN WILD-TYPE 88  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    0
  19P GAIN WILD-TYPE   88    9
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                2                 88
  1                0                  9
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1   3
  19P GAIN WILD-TYPE  71 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    3
  19P GAIN WILD-TYPE   71  194
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                1                 71
  MALE                  3                194
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 59 
        TCGA-2Z-A9JK         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-A4-8310 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-8630         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-5560         TCGA-DW-5561 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-P4-AAVK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D33V9, continuous
D33V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           0     4
  19P GAIN WILD-TYPE                        60   183
D33V11, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 60
  WHITE                                           4                183
[1] 4 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   4
  19P GAIN WILD-TYPE  12 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    4
  19P GAIN WILD-TYPE   12  216
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                4                216
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED     4   0
  19Q GAIN WILD-TYPE 218  34
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                252 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                 34 
$`19Q GAIN MUTATED`
TCGA-BQ-5885 TCGA-BQ-5892 TCGA-G7-A8LC TCGA-GL-7966 
       30.28        11.97        17.33         3.68 

$`19Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        26.04        25.35        13.25        10.88 
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-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        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        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         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 
            14.650             21.535 
[1] "3.7 - 30.3 (14.6)"  "0.1 - 194.8 (21.5)"
[1] "hr="     "3300000"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         2        0         2        0
  19Q GAIN WILD-TYPE     165       21        47       14
D34V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  2                165
  STAGE II                 0                 21
  STAGE III                2                 47
  STAGE IV                 0                 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 GAIN MUTATED     2   0     2
  19Q GAIN WILD-TYPE 174  29    54
D34V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                   2                174
  T2                   0                 29
  T3+T4                2                 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
  19Q GAIN MUTATED    2  1  0
  19Q GAIN WILD-TYPE 43 21  4
D34V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                2                 43
  N1                1                 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"
D34V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  0
  19Q GAIN WILD-TYPE 88  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    0
  19Q GAIN WILD-TYPE   88    9
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                2                 88
  1                0                  9
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1   3
  19Q GAIN WILD-TYPE  71 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    3
  19Q GAIN WILD-TYPE   71  194
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                 71
  MALE                  3                194
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 59 
        TCGA-2Z-A9JK         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-A4-8310 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-8630         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-5560         TCGA-DW-5561 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-P4-AAVK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D34V9, continuous
D34V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           0     4
  19Q GAIN WILD-TYPE                        60   183
D34V11, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 60
  WHITE                                           4                183
[1] 4 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   4
  19Q GAIN WILD-TYPE  12 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    4
  19Q GAIN WILD-TYPE   12  216
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                4                216
[1] 2 2
[1] FALSE

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    76   9
  20P GAIN WILD-TYPE 146  25
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                85                171 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 9                 25 
$`20P GAIN MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9JG TCGA-2Z-A9JM TCGA-2Z-A9JS 
        7.04        75.55         4.57        54.64        30.71        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 
       22.49         0.13        12.82        18.21        19.13         0.89 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8517 TCGA-A4-8518 
       16.64        30.48        25.64        23.97        19.63        19.73 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 
       16.31        15.75        12.99         9.63        76.64        13.55 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4103 
        2.20         7.33        24.56         3.55        33.83        30.58 
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-5882 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
       21.63        25.35         0.95        11.97         2.76        96.92 
TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 
       50.40         3.81        11.61        13.61        35.93        14.63 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6789 
       80.88        51.19        19.00        13.08         2.40         4.01 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NF 
       39.25        25.15        17.98        17.33         3.68        68.12 
TCGA-HE-A5NI TCGA-IA-A40Y TCGA-IZ-8195 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       11.84         2.04        22.26        11.97        29.10        34.29 
TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       20.25         0.36         6.61        52.27        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS 
       47.90        28.80        27.06        16.31        41.62        48.30 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A895 
        0.53        52.11        25.68        12.99        29.00        15.91 
TCGA-Y8-A8S0 
        6.02 

$`20P GAIN WILD-TYPE`
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       59.01        58.22       100.27        56.91        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       34.85        56.81        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-4A-A93Y 
       24.33        31.20        29.36        25.58         5.29        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
       19.63        61.05         0.10        35.18         0.23        29.46 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.28        23.31         0.76        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.48         8.28        12.46        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A655 
       44.61        49.25        19.56        21.67        16.87        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-A6W5 TCGA-B9-4113 
        0.46         6.58        10.09        34.49        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A44B 
       28.18        26.40        20.61        15.12        43.99         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81        14.86        12.30        86.76        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-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.88         7.66 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        7.92       123.62        48.26        93.34        44.84        61.28 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        7.17       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        40.77        79.86        61.02        54.90        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       24.89        10.68         1.18         0.43        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
       11.05        34.82        13.68        25.84         6.38        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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ 
       17.95         0.89        11.21         4.60        13.41        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A74V 
       67.17        21.34        16.34        12.36         0.13        11.41 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.78        30.38        27.65        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        12.85        47.44        33.04 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 
       11.93        19.00        38.63        26.47        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PU 
       60.03        14.83        21.93        86.27        38.86        30.67 
TCGA-UZ-A9PX TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       27.39        26.01        18.64        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       25.28         6.74        13.28 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.13               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             96.92             194.79 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             17.49              24.89 
[1] "0.1 - 96.9 (17.5)"  "0.1 - 194.8 (24.9)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED        57        9        14        5
  20P GAIN WILD-TYPE     110       12        35        9
D35V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 57                110
  STAGE II                 9                 12
  STAGE III               14                 35
  STAGE IV                 5                  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    60  13    16
  20P GAIN WILD-TYPE 116  16    40
D35V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                  60                116
  T2                  13                 16
  T3+T4               16                 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
  20P GAIN MUTATED   12  7  1
  20P GAIN WILD-TYPE 33 15  3
D35V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               12                 33
  N1                7                 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"
D35V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   31  3
  20P GAIN WILD-TYPE 59  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     31    3
  20P GAIN WILD-TYPE   59    6
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               31                 59
  1                3                  6
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    25  66
  20P GAIN WILD-TYPE  47 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     25   66
  20P GAIN WILD-TYPE   47  131
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               25                 47
  MALE                 66                131
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     1
  20P GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          15    67
  20P GAIN WILD-TYPE                        45   120
D35V11, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                      15                 45
  WHITE                                          67                120
[1] 4 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  76
  20P GAIN WILD-TYPE   9 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   76
  20P GAIN WILD-TYPE    9  144
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               76                144
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    77  10
  20Q GAIN WILD-TYPE 145  24
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                87                169 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 24 
$`20Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9JG TCGA-2Z-A9JM TCGA-2Z-A9JS 
        7.04        75.55         4.57        54.64        30.71        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 
       22.49         0.13        12.82        18.21        19.13         0.89 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8517 TCGA-A4-8518 
       16.64        30.48        25.64        23.97        19.63        19.73 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 
       16.31        15.75        12.99         9.63        76.64        13.55 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4103 
        2.20         7.33        24.56         3.55        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-7268 TCGA-B9-A5W9 
       34.49        12.46         0.46         1.15        22.06         0.16 
TCGA-B9-A8YH TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 
       17.49        22.92        21.63        25.35         0.95        11.97 
TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        2.76        96.92        50.40         3.81        11.61        13.61 
TCGA-DW-7836 TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7Q0 
       35.93        14.63        80.88        51.19        19.00        13.08 
TCGA-F9-A7VF TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC 
        2.40         4.01        39.25        25.15        17.98        17.33 
TCGA-GL-7966 TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40Y TCGA-IZ-8195 TCGA-KV-A6GD 
        3.68        68.12        11.84         2.04        22.26        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EA TCGA-P4-AAVK 
       29.10        34.29        20.25         0.36         6.61        52.27 
TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71V TCGA-SX-A7SL 
       78.90        17.75        14.07        47.90        28.80        27.06 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PP TCGA-UZ-A9PV TCGA-UZ-A9Q0 
       16.31        41.62        48.30         0.53        25.68        12.99 
TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A8S0 
       29.00        15.91         6.02 

$`20Q GAIN WILD-TYPE`
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       59.01        58.22       100.27        56.91        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       34.85        56.81        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-4A-A93Y 
       24.33        31.20        29.36        25.58         5.29        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
       19.63        61.05         0.10        35.18         0.23        29.46 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.28        23.31         0.76        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.48         8.28        12.46        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A655 
       44.61        49.25        19.56        21.67        16.87        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
        0.46         6.58        10.09        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 
       26.40        20.61        15.12        43.99         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81        14.86        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7044 
       26.04        13.25        10.88         7.66         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
       48.26        93.34        44.84        61.28        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7834 
       20.12        11.28         7.63         7.04         7.17       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46        13.78         3.75         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
       79.86        61.02        54.90        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        48.62        11.05        34.82 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       13.68        25.84         6.38        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       11.21         4.60        13.41        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 
       16.80        19.99        85.78        88.24        67.17        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 
       16.34        12.36         0.13        11.41        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       87.22        42.94        84.95        92.58        16.01        50.60 
TCGA-PJ-A5Z8 TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       12.85        47.44        33.04        11.93        19.00        38.63 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-WN-A9G9 
       86.27        38.86        52.11        30.67        27.39        26.01 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       18.64        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S1 
       13.28 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.13               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             96.92             194.79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             17.75              24.89 
[1] "0.1 - 96.9 (17.8)"  "0.1 - 194.8 (24.9)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED        57        9        15        5
  20Q GAIN WILD-TYPE     110       12        34        9
D36V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 57                110
  STAGE II                 9                 12
  STAGE III               15                 34
  STAGE IV                 5                  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    60  13    17
  20Q GAIN WILD-TYPE 116  16    39
D36V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                  60                116
  T2                  13                 16
  T3+T4               17                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  20Q GAIN MUTATED   12  8  1
  20Q GAIN WILD-TYPE 33 14  3
D36V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               12                 33
  N1                8                 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"
D36V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   33  3
  20Q GAIN WILD-TYPE 57  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     33    3
  20Q GAIN WILD-TYPE   57    6
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               33                 57
  1                3                  6
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    25  68
  20Q GAIN WILD-TYPE  47 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     25   68
  20Q GAIN WILD-TYPE   47  129
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               25                 47
  MALE                 68                129
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     1
  20Q GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          14    70
  20Q GAIN WILD-TYPE                        46   117
D36V11, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                      14                 46
  WHITE                                          70                117
[1] 4 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  77
  20Q GAIN WILD-TYPE   9 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   77
  20Q GAIN WILD-TYPE    9  143
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               77                143
[1] 2 2
[1] FALSE

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    15   2
  21Q GAIN WILD-TYPE 207  32
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                17                239 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 32 
$`21Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9JS TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-A6HP TCGA-AT-A5NU 
        7.04        16.18        23.97        23.31        12.46         2.20 
TCGA-B1-A47O TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-F9-A8NY TCGA-G7-A8LC 
       16.87         0.46         0.16        11.97         1.18        17.33 
TCGA-HE-A5NJ TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UZ-A9PK TCGA-UZ-A9Q0 
       56.75         6.61        14.07        60.03        12.99 

$`21Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       29.36        25.58         5.29        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       25.64        23.28         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-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.99         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       25.08        44.61        49.25        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40        20.61         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06         2.10        19.23         6.81        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       10.68        13.08         2.40         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       21.44        15.48        99.78        87.22        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        18.02        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.16               0.10 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             60.03             194.79 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             12.99              22.06 
[1] "0.2 - 60.0 (13.0)"  "0.1 - 194.8 (22.1)"
[1] "hr=" "1.6"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED        12        1         3        1
  21Q GAIN WILD-TYPE     155       20        46       13
D37V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                 12                155
  STAGE II                 1                 20
  STAGE III                3                 46
  STAGE IV                 1                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  21Q GAIN MUTATED    13   2     4
  21Q GAIN WILD-TYPE 163  27    52
D37V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                  13                163
  T2                   2                 27
  T3+T4                4                 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
  21Q GAIN MUTATED    2  2  0
  21Q GAIN WILD-TYPE 43 20  4
D37V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                2                 43
  N1                2                 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"
D37V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  1
  21Q GAIN WILD-TYPE 87  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    1
  21Q GAIN WILD-TYPE   87    8
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                3                 87
  1                1                  8
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     5  14
  21Q GAIN WILD-TYPE  67 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5   14
  21Q GAIN WILD-TYPE   67  183
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                5                 67
  MALE                 14                183
[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                 49 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         TCGA-2Z-A9JN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-5561         TCGA-DW-7963 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-7501         TCGA-G7-A8LB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"21Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1     1
  21Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           3    13
  21Q GAIN WILD-TYPE                        57   174
D37V11, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       3                 57
  WHITE                                          13                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"
D37V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  17
  21Q GAIN WILD-TYPE  11 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   17
  21Q GAIN WILD-TYPE   11  203
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               17                203
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     2   0
  22Q GAIN WILD-TYPE 220  34
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                254 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                 34 
$`22Q GAIN MUTATED`
TCGA-BQ-5892 TCGA-G7-A8LB 
       11.97        17.98 

$`22Q GAIN WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
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-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
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        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.33        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             11.97               0.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             17.98             194.79 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            14.975             21.535 
[1] "12.0 - 18.0 (15.0)" "0.1 - 194.8 (21.5)"
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         2        0         0        1
  22Q GAIN WILD-TYPE     165       21        49       13
D38V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  2                165
  STAGE II                 0                 21
  STAGE III                0                 49
  STAGE IV                 1                 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
  22Q GAIN MUTATED     2   1     0
  22Q GAIN WILD-TYPE 174  28    56
D38V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                   2                174
  T2                   1                 28
  T3+T4                0                 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
  22Q GAIN MUTATED    1  0  0
  22Q GAIN WILD-TYPE 44 22  4
D38V5, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 70 
        TCGA-2Z-A9J1         TCGA-2Z-A9JO         TCGA-4A-A93W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y1         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-A47O 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B1-A657 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5888 
"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-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-F9-A97G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6789         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-GL-6846 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-A59R         TCGA-GL-A9DC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40Y         TCGA-IA-A83W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-KV-A74V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-A5E8         TCGA-P4-A5EA 
"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" 
        TCGA-Y8-A8RZ 
"22Q GAIN WILD-TYPE" 
D38V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    1  0
  22Q GAIN WILD-TYPE 89  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    0
  22Q GAIN WILD-TYPE   89    9
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                1                 89
  1                0                  9
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0   3
  22Q GAIN WILD-TYPE  72 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    3
  22Q GAIN WILD-TYPE   72  194
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                0                 72
  MALE                  3                194
[1] 2 2
[1] FALSE
D38V8, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 59 
        TCGA-2Z-A9JK         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-A4-8310 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-8630         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-5560         TCGA-DW-5561 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         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-A7SO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU 
"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                 64 
        TCGA-2Z-A9J2         TCGA-2Z-A9J5         TCGA-2Z-A9J7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         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-2Z-A9JQ         TCGA-4A-A93W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-8310         TCGA-A4-A48D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3466 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-7268 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-B9-A69E         TCGA-DW-5561 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7963         TCGA-F9-A97G 
"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-A59T         TCGA-GL-A9DD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"22Q GAIN WILD-TYPE" 
D38V10, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 50 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         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-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         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-IA-A40U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"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     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           0     3
  22Q GAIN WILD-TYPE                        60   184
D38V11, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 60
  WHITE                                           3                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"
D38V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1   2
  22Q GAIN WILD-TYPE  11 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    2
  22Q GAIN WILD-TYPE   11  218
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                2                218
[1] 2 2
[1] FALSE

Clustering(39) Variable = XP GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    68   8
  XP GAIN WILD-TYPE 154  26
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               76               180 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                8                26 
$`XP GAIN MUTATED`
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JQ 
       75.55        59.01        58.22       100.27        56.91        25.58 
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-3468 TCGA-AL-3471 
       16.96        16.31        15.75        12.46        76.64        13.55 
TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 
        2.20        21.67        24.56         6.58        30.58        10.16 
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-7046 
       17.49        47.80         0.95         7.92        48.26        96.92 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF 
        7.04         3.81        35.93        40.77        51.19         2.40 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 
        1.18        51.78        39.25         6.38        17.98       194.79 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD 
       17.95        68.12        11.84        56.75         5.49        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-P4-A5E7 TCGA-P4-A5EB 
       29.10        11.41        34.29        27.78        87.22        84.95 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN 
       52.27        16.01        17.75        33.04        28.80        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PU 
       16.31        41.62        26.47        48.30        60.03        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       25.68        27.39        12.99        15.91 

$`XP GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
        7.04         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       24.33        31.20        29.36         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E 
       30.48        29.46        25.64        23.28        19.73         8.48 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.99         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A654 
       44.61        49.25        19.56         7.33        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       16.77         0.46        33.83        10.09        34.49        12.46 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       26.40        20.61        15.12        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81        14.86        12.30        86.76        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
       11.97         2.76       123.62        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        7.17        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.78         3.75        14.63         3.02        79.86        80.88 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
       13.08         0.43         4.01        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.15        13.68        25.84        17.33        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         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
       11.21         4.60        13.41        73.25        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       16.34        12.36         0.13        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       42.94         6.61        92.58        50.60        78.90        12.85 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO 
       14.07        47.90        47.44        27.06        11.93        38.63 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        18.02        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       38.86        52.11        26.01        29.00        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        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 
           24.265            20.185 
[1] "0.2 - 194.8 (24.3)" "0.1 - 129.9 (20.2)"
[1] "hr=" "1.5"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED        62        5         4        4
  XP GAIN WILD-TYPE     105       16        45       10
D39V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                62               105
  STAGE II                5                16
  STAGE III               4                45
  STAGE IV                4                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  XP GAIN MUTATED    64   9     7
  XP GAIN WILD-TYPE 112  20    49
D39V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T1                 64               112
  T2                  9                20
  T3+T4               7                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
  XP GAIN MUTATED   10  3  0
  XP GAIN WILD-TYPE 35 19  4
D39V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              10                35
  N1               3                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"
D39V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   25  2
  XP GAIN WILD-TYPE 65  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     25    2
  XP GAIN WILD-TYPE   65    7
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              25                65
  1               2                 7
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    15  67
  XP GAIN WILD-TYPE  57 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     15   67
  XP GAIN WILD-TYPE   57  130
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              15                57
  MALE                67               130
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                          14    58
  XP GAIN WILD-TYPE                        46   129
D39V11, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                     14                46
  WHITE                                         58               129
[1] 4 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  68
  XP GAIN WILD-TYPE   8 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      4   68
  XP GAIN WILD-TYPE    8  152
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO              68               152
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    71   8
  XQ GAIN WILD-TYPE 151  26
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               79               177 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                8                26 
$`XQ GAIN MUTATED`
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JQ 
       75.55        59.01        58.22       100.27        56.91        25.58 
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-3468 TCGA-AL-3471 
       16.96        16.31        15.75        12.46        76.64        13.55 
TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 
        2.20        21.67        24.56         6.58        30.58        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        20.61         0.46         1.15        43.99 
TCGA-B9-A44B TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 
        2.10         0.16        17.49        47.80        25.35         0.95 
TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 
        7.92        48.26        96.92         7.04         3.81        35.93 
TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6795 
       40.77        51.19         2.40         1.18        51.78        39.25 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI 
        6.38        17.98       194.79        17.95        68.12        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       56.75         5.49        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 
       27.78        87.22        84.95        52.27        16.01        17.75 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       33.04        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 
       48.30        60.03        30.67        25.68        27.39        12.99 
TCGA-Y8-A895 
       15.91 

$`XQ GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
        7.04         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       24.33        31.20        29.36         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E 
       30.48        29.46        25.64        23.28        19.73         8.48 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.99         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A654 
       44.61        49.25        19.56         7.33        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       16.77         0.46        33.83        10.09        34.49        12.46 
TCGA-B9-4115 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
       26.40        15.12        22.06        19.23         6.81        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-5886 
       43.20        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
       13.25        10.88         7.66        11.97         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 
       20.12        11.28         7.63         7.17        11.61        13.61 
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-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        79.86        80.88        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 
       19.00        24.89        10.68        13.08         0.43         4.01 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        34.82        25.15        13.68        25.84 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       17.33        16.90        80.65        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH 
        1.05        12.43         0.89        11.21         4.60        13.41 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       73.25        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       21.44        15.48        99.78        42.94         6.61        92.58 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       50.60        78.90        12.85        14.07        47.90        47.44 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM 
       27.06        11.93        38.63        43.76        18.02        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-WN-A9G9 
       21.93         0.53        86.27        38.86        52.11        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         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 
            23.97             20.12 
[1] "0.2 - 194.8 (24.0)" "0.1 - 129.9 (20.1)"
[1] "hr=" "1.6"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED        62        5         6        4
  XQ GAIN WILD-TYPE     105       16        43       10
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                62               105
  STAGE II                5                16
  STAGE III               6                43
  STAGE IV                4                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
  XQ GAIN MUTATED    64  10     9
  XQ GAIN WILD-TYPE 112  19    47
D40V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                 64               112
  T2                 10                19
  T3+T4               9                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
  XQ GAIN MUTATED   11  3  0
  XQ GAIN WILD-TYPE 34 19  4
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              11                34
  N1               3                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"
D40V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   26  2
  XQ GAIN WILD-TYPE 64  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     26    2
  XQ GAIN WILD-TYPE   64    7
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              26                64
  1               2                 7
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    16  69
  XQ GAIN WILD-TYPE  56 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     16   69
  XQ GAIN WILD-TYPE   56  128
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              16                56
  MALE                69               128
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          16    59
  XQ GAIN WILD-TYPE                        44   128
D40V11, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                     16                44
  WHITE                                         59               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"
D40V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     4  70
  XQ GAIN WILD-TYPE   8 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4   70
  XQ GAIN WILD-TYPE    8  150
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO              70               150
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    22   4
  1P LOSS WILD-TYPE 200  30
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               26               230 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4                30 
$`1P LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 
       54.64        51.52        12.82        18.21         0.10        29.46 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5894 
        7.33        10.09         6.81        86.76        21.63         2.76 
TCGA-BQ-7044 TCGA-BQ-7055 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6797 TCGA-G7-7502 
      123.62        26.27        10.68        13.08        25.15        25.84 
TCGA-G7-A8LC TCGA-GL-8500 TCGA-HE-A5NK TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       17.33        27.65        73.25         6.61        12.85        14.07 
TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       18.02        86.27 

$`1P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05        35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       44.61        49.25         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06         2.10        19.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       19.00        24.89         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        48.62        11.05        39.25        34.82        13.68 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
        4.60        68.12        13.41        11.84        56.75         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.22        42.94        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK 
       16.31        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       14.83        21.93         0.53        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        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 
           18.115            21.555 
[1] "0.1 - 123.6 (18.1)" "0.1 - 194.8 (21.6)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED        11        2         9        1
  1P LOSS WILD-TYPE     156       19        40       13
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                11               156
  STAGE II                2                19
  STAGE III               9                40
  STAGE IV                1                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    13   3     9
  1P LOSS WILD-TYPE 163  26    47
D41V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                 13               163
  T2                  3                26
  T3+T4               9                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
  1P LOSS MUTATED    3  3  0
  1P LOSS WILD-TYPE 42 19  4
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               3                42
  N1               3                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"
D41V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   10  1
  1P LOSS WILD-TYPE 80  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10    1
  1P LOSS WILD-TYPE   80    8
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              10                80
  1               1                 8
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     9  17
  1P LOSS WILD-TYPE  63 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      9   17
  1P LOSS WILD-TYPE   63  180
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               9                63
  MALE                17               180
[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                49 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117        TCGA-B9-A69E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-PJ-A5Z9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-UZ-A9PR        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" 
       TCGA-Y8-A8RZ 
"1P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           8    14
  1P LOSS WILD-TYPE                        52   173
D41V11, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      8                52
  WHITE                                         14               173
[1] 4 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  19
  1P LOSS WILD-TYPE  11 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   19
  1P LOSS WILD-TYPE   11  201
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              19               201
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    18   1
  1Q LOSS WILD-TYPE 204  33
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               19               237 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                33 
$`1Q LOSS MUTATED`
TCGA-2Z-A9JG TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-7332 TCGA-B1-A655 
       54.64        12.82        18.21         0.10         7.33        16.77 
TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5894 TCGA-F9-A7Q0 TCGA-G7-6797 TCGA-G7-7502 
       10.09         6.81         2.76        13.08        25.15        25.84 
TCGA-G7-A8LC TCGA-GL-8500 TCGA-HE-A5NK TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       17.33        27.65        73.25         6.61        12.85        14.07 
TCGA-UN-AAZ9 
       18.02 

$`1Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI 
        4.57        67.30        75.42        34.85        56.81        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       11.57        19.63        61.05        35.18        19.13         0.89 
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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        16.87         3.55         0.46         6.58 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06         2.10        19.23         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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.92       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        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        48.62        11.05        39.25        34.82        13.68 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
        4.60        68.12        13.41        11.84        56.75         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.22        42.94        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK 
       16.31        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         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 
            14.07             22.06 
[1] "0.1 - 73.2 (14.1)"  "0.1 - 194.8 (22.1)"
[1] "hr=" "1.6"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED        10        2         3        1
  1Q LOSS WILD-TYPE     157       19        46       13
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                10               157
  STAGE II                2                19
  STAGE III               3                46
  STAGE IV                1                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    12   2     4
  1Q LOSS WILD-TYPE 164  27    52
D42V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1                 12               164
  T2                  2                27
  T3+T4               4                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
  1Q LOSS MUTATED    3  2  0
  1Q LOSS WILD-TYPE 42 20  4
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               3                42
  N1               2                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"
D42V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    7  1
  1Q LOSS WILD-TYPE 83  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7    1
  1Q LOSS WILD-TYPE   83    8
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               7                83
  1               1                 8
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     8  11
  1Q LOSS WILD-TYPE  64 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8   11
  1Q LOSS WILD-TYPE   64  186
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               8                64
  MALE                11               186
[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                63 
       TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JD        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-2Z-A9JQ        TCGA-4A-A93W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-8310        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-3466        TCGA-AL-3472        TCGA-AL-7173 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4115        TCGA-B9-4117        TCGA-B9-7268 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7834 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501        TCGA-G7-A8LB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-IA-A40U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854        TCGA-MH-A856 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        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-A9PO        TCGA-UZ-A9PR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RY        TCGA-Y8-A8RZ 
"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                50 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7963        TCGA-F9-A97G 
"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-IA-A40U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        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        TCGA-Y8-A8RZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           5    11
  1Q LOSS WILD-TYPE                        55   176
D42V11, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      5                55
  WHITE                                         11               176
[1] 4 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  17
  1Q LOSS WILD-TYPE  11 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   17
  1Q LOSS WILD-TYPE   11  203
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              17               203
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     2   0
  2P LOSS WILD-TYPE 220  34
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               254 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                34 
$`2P LOSS MUTATED`
TCGA-4A-A93X TCGA-BQ-5875 
       12.82        86.76 

$`2P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        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        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.33        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        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 
            49.79             21.39 
[1] "12.8 - 86.8 (49.8)" "0.1 - 194.8 (21.4)"
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
D43V2, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               262 
       TCGA-2K-A9WE        TCGA-2Z-A9J1        TCGA-2Z-A9J2        TCGA-2Z-A9J3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9J5        TCGA-2Z-A9J6        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9J9        TCGA-2Z-A9JD        TCGA-2Z-A9JE        TCGA-2Z-A9JG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JJ        TCGA-2Z-A9JK        TCGA-2Z-A9JL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JM        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JQ        TCGA-2Z-A9JR        TCGA-2Z-A9JS        TCGA-2Z-A9JT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-7286        TCGA-A4-7287 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7288        TCGA-A4-7583        TCGA-A4-7584        TCGA-A4-7585 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7828        TCGA-A4-7915 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-7997        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-A4-8515        TCGA-A4-8516 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-8517        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-A4-A5Y1        TCGA-A4-A6HP        TCGA-A4-A772 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A7UZ        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AL-A5DJ        TCGA-AT-A5NU        TCGA-B1-5398        TCGA-B1-7332 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A47M        TCGA-B1-A47N        TCGA-B1-A47O        TCGA-B1-A654 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A655        TCGA-B1-A656        TCGA-B1-A657        TCGA-B3-3925 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B3-A6W5        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-5156        TCGA-B9-7268        TCGA-B9-A44B        TCGA-B9-A5W7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-B9-A69E        TCGA-B9-A8YH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-A8YI        TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        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-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        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-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-F9-A4JJ        TCGA-F9-A7Q0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F9-A7VF        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-G7-6790        TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-6846        TCGA-GL-7773        TCGA-GL-7966 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-A9DC        TCGA-GL-A9DD        TCGA-GL-A9DE        TCGA-HE-A5NF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HE-A5NH        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-HE-A5NL        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IA-A83T        TCGA-IA-A83W        TCGA-IZ-8195 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-IZ-A6M8        TCGA-IZ-A6M9        TCGA-J7-6720 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-J7-8537        TCGA-KV-A6GD        TCGA-KV-A6GE        TCGA-KV-A74V 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A55W        TCGA-MH-A55Z        TCGA-MH-A560        TCGA-MH-A561 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A562        TCGA-MH-A854        TCGA-MH-A855        TCGA-MH-A856 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A857        TCGA-O9-A75Z        TCGA-P4-A5E6        TCGA-P4-A5E7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-A5E8        TCGA-P4-A5EA        TCGA-P4-A5EB        TCGA-P4-A5ED 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-P4-AAVL        TCGA-P4-AAVM        TCGA-P4-AAVO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-PJ-A5Z8        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ        TCGA-SX-A71R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UN-AAZ9        TCGA-UZ-A9PJ        TCGA-UZ-A9PK        TCGA-UZ-A9PL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PN        TCGA-UZ-A9PO        TCGA-UZ-A9PP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PQ        TCGA-UZ-A9PR        TCGA-UZ-A9PS        TCGA-UZ-A9PU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PV        TCGA-UZ-A9PX        TCGA-UZ-A9PZ        TCGA-UZ-A9Q0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9Q1        TCGA-Y8-A894        TCGA-Y8-A895        TCGA-Y8-A896 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A897        TCGA-Y8-A898        TCGA-Y8-A8RY        TCGA-Y8-A8RZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A8S0        TCGA-Y8-A8S1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         0        0         2        0
  2P LOSS WILD-TYPE     167       21        47       14
D43V3, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               249 
       TCGA-2K-A9WE        TCGA-2Z-A9J1        TCGA-2Z-A9J2        TCGA-2Z-A9J3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9J5        TCGA-2Z-A9J6        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9J9        TCGA-2Z-A9JD        TCGA-2Z-A9JE        TCGA-2Z-A9JG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JJ        TCGA-2Z-A9JK        TCGA-2Z-A9JL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JM        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JQ        TCGA-2Z-A9JR        TCGA-2Z-A9JS        TCGA-2Z-A9JT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-4A-A93W        TCGA-A4-7287        TCGA-A4-7583        TCGA-A4-7584 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7734        TCGA-A4-7828        TCGA-A4-7915 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-7997        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-A4-8515        TCGA-A4-8516 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-8517        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-A4-A5Y1        TCGA-A4-A6HP        TCGA-A4-A772 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A7UZ        TCGA-AL-3466        TCGA-AL-3468        TCGA-AL-3471 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AL-3473        TCGA-AL-7173        TCGA-AL-A5DJ        TCGA-AT-A5NU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B1-A47M        TCGA-B1-A47N 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A47O        TCGA-B1-A654        TCGA-B1-A655        TCGA-B1-A656 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A657        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B3-8121        TCGA-B3-A6W5        TCGA-B9-4113 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-4115        TCGA-B9-5155        TCGA-B9-7268        TCGA-B9-A44B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-A5W7        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-B9-A69E 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-A8YH        TCGA-B9-A8YI        TCGA-BQ-5876        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-5881 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-DZ-6131 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-F9-A4JJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F9-A7Q0        TCGA-F9-A7VF        TCGA-F9-A8NY        TCGA-F9-A97G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-6846        TCGA-GL-7773 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-A59T        TCGA-GL-A9DC        TCGA-GL-A9DD        TCGA-GL-A9DE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HE-7128        TCGA-HE-7129        TCGA-HE-A5NF        TCGA-HE-A5NH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NL        TCGA-IA-A40U        TCGA-IA-A40X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-IA-A83S        TCGA-IA-A83T        TCGA-IA-A83W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IZ-8195        TCGA-IZ-8196        TCGA-IZ-A6M8        TCGA-IZ-A6M9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-J7-6720        TCGA-J7-8537        TCGA-KV-A6GD        TCGA-KV-A6GE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KV-A74V        TCGA-MH-A55W        TCGA-MH-A55Z        TCGA-MH-A560 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A561        TCGA-MH-A562        TCGA-MH-A854        TCGA-MH-A855 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-MH-A857        TCGA-O9-A75Z        TCGA-P4-A5E6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5E8        TCGA-P4-A5EA        TCGA-P4-A5EB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-A5ED        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SO 
"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-UN-AAZ9        TCGA-UZ-A9PJ        TCGA-UZ-A9PK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PL        TCGA-UZ-A9PM        TCGA-UZ-A9PN        TCGA-UZ-A9PO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PP        TCGA-UZ-A9PQ        TCGA-UZ-A9PR        TCGA-UZ-A9PS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PU        TCGA-UZ-A9PV        TCGA-UZ-A9PX        TCGA-UZ-A9PZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9Q0        TCGA-UZ-A9Q1        TCGA-WN-A9G9        TCGA-WN-AB4C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A894        TCGA-Y8-A895        TCGA-Y8-A896        TCGA-Y8-A897 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A898        TCGA-Y8-A8RY        TCGA-Y8-A8RZ        TCGA-Y8-A8S0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A8S1 
"2P LOSS WILD-TYPE" 
                   vv
clus                 T1  T2 T3+T4
  2P LOSS MUTATED     0   0     2
  2P LOSS WILD-TYPE 176  29    54
D43V4, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               259 
       TCGA-2K-A9WE        TCGA-2Z-A9J1        TCGA-2Z-A9J2        TCGA-2Z-A9J3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9J5        TCGA-2Z-A9J6        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9J9        TCGA-2Z-A9JD        TCGA-2Z-A9JE        TCGA-2Z-A9JG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JJ        TCGA-2Z-A9JK        TCGA-2Z-A9JL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JM        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JQ        TCGA-2Z-A9JR        TCGA-2Z-A9JS        TCGA-2Z-A9JT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-4A-A93W        TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7583        TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7734        TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7997        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A5Y0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A5Y1        TCGA-A4-A6HP        TCGA-A4-A772        TCGA-A4-A7UZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"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-AL-A5DJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AT-A5NU        TCGA-B1-5398        TCGA-B1-7332        TCGA-B1-A47M 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A47N        TCGA-B1-A47O        TCGA-B1-A654        TCGA-B1-A655 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A656        TCGA-B1-A657        TCGA-B3-3925        TCGA-B3-3926 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B3-A6W5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A44B        TCGA-B9-A5W7        TCGA-B9-A5W8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-A5W9        TCGA-B9-A69E        TCGA-B9-A8YH        TCGA-B9-A8YI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-F9-A4JJ        TCGA-F9-A7Q0        TCGA-F9-A7VF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F9-A8NY        TCGA-F9-A97G        TCGA-G7-6789        TCGA-G7-6790 
"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-G7-6796 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-6846        TCGA-GL-7773        TCGA-GL-7966        TCGA-GL-8500 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T        TCGA-GL-A9DC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-GL-A9DE        TCGA-HE-7128        TCGA-HE-7129 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HE-A5NF        TCGA-HE-A5NH        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HE-A5NK        TCGA-HE-A5NL        TCGA-IA-A40U        TCGA-IA-A40X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-IA-A83W        TCGA-IZ-8195        TCGA-IZ-8196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-IZ-A6M9        TCGA-J7-6720        TCGA-J7-8537 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KV-A6GD        TCGA-KV-A6GE        TCGA-KV-A74V        TCGA-MH-A55W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A55Z        TCGA-MH-A560        TCGA-MH-A561        TCGA-MH-A562 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A855        TCGA-MH-A856        TCGA-MH-A857 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-O9-A75Z        TCGA-P4-A5E6        TCGA-P4-A5E7        TCGA-P4-A5E8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-A5EA        TCGA-P4-A5EB        TCGA-P4-A5ED        TCGA-PJ-A5Z8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU        TCGA-UN-AAZ9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PJ        TCGA-UZ-A9PK        TCGA-UZ-A9PL        TCGA-UZ-A9PM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PN        TCGA-UZ-A9PO        TCGA-UZ-A9PP        TCGA-UZ-A9PQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-UZ-A9PS        TCGA-UZ-A9PU        TCGA-UZ-A9PV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-UZ-A9PZ        TCGA-UZ-A9Q0        TCGA-UZ-A9Q1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-WN-A9G9        TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A895 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A897        TCGA-Y8-A898        TCGA-Y8-A8RY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-Y8-A8S0        TCGA-Y8-A8S1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                N0 N1 N2
  2P LOSS MUTATED    0  0  0
  2P LOSS WILD-TYPE 45 22  4
D43V5, multiclass
D43V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    2  0
  2P LOSS WILD-TYPE 88  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    0
  2P LOSS WILD-TYPE   88    9
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               2                88
  1               0                 9
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2   1
  2P LOSS WILD-TYPE  70 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    1
  2P LOSS WILD-TYPE   70  196
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                70
  MALE                 1               196
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                59 
       TCGA-2Z-A9JK        TCGA-4A-A93Y        TCGA-A4-7286        TCGA-A4-7828 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466        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-DW-7963        TCGA-EV-5901        TCGA-EV-5902 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V9, continuous
D43V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0     2
  2P LOSS WILD-TYPE                        60   185
D43V11, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               252 
       TCGA-2K-A9WE        TCGA-2Z-A9J1        TCGA-2Z-A9J2        TCGA-2Z-A9J3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9J5        TCGA-2Z-A9J6        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9J9        TCGA-2Z-A9JD        TCGA-2Z-A9JE        TCGA-2Z-A9JG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JJ        TCGA-2Z-A9JK        TCGA-2Z-A9JL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JM        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-2Z-A9JQ        TCGA-2Z-A9JR        TCGA-2Z-A9JS        TCGA-2Z-A9JT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-7286        TCGA-A4-7287 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7288        TCGA-A4-7583        TCGA-A4-7584        TCGA-A4-7585 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7828        TCGA-A4-7915 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-7997        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-A4-8515        TCGA-A4-8516 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-8517        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-A4-A5Y1        TCGA-A4-A6HP        TCGA-A4-A772 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A4-A7UZ        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AL-A5DJ        TCGA-AT-A5NU        TCGA-B1-5398        TCGA-B1-7332 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A47M        TCGA-B1-A47N        TCGA-B1-A47O        TCGA-B1-A654 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B1-A655        TCGA-B1-A656        TCGA-B1-A657        TCGA-B3-3925 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B3-A6W5        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-5156        TCGA-B9-7268        TCGA-B9-A44B        TCGA-B9-A5W7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-B9-A69E        TCGA-B9-A8YH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B9-A8YI        TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5883 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-7044        TCGA-BQ-7045 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6133        TCGA-DZ-6134        TCGA-EV-5901 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-F9-A4JJ        TCGA-F9-A7Q0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F9-A7VF        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-G7-6790        TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-6846        TCGA-GL-7773        TCGA-GL-7966 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GL-A9DC        TCGA-GL-A9DD        TCGA-GL-A9DE        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-IA-A83S        TCGA-IA-A83T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IA-A83W        TCGA-IZ-8195        TCGA-IZ-8196        TCGA-IZ-A6M8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IZ-A6M9        TCGA-J7-6720        TCGA-J7-8537        TCGA-KV-A6GD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KV-A6GE        TCGA-KV-A74V        TCGA-MH-A55W        TCGA-MH-A55Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A560        TCGA-MH-A561        TCGA-MH-A562        TCGA-MH-A854 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MH-A855        TCGA-MH-A856        TCGA-MH-A857        TCGA-O9-A75Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-A5E7        TCGA-P4-A5E8        TCGA-P4-A5EA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-P4-A5ED        TCGA-P4-AAVK        TCGA-P4-AAVL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-P4-AAVM        TCGA-P4-AAVO        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"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-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SO 
"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-UN-AAZ9        TCGA-UZ-A9PJ        TCGA-UZ-A9PK        TCGA-UZ-A9PL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PN        TCGA-UZ-A9PO        TCGA-UZ-A9PP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PQ        TCGA-UZ-A9PR        TCGA-UZ-A9PS        TCGA-UZ-A9PU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9PV        TCGA-UZ-A9PX        TCGA-UZ-A9PZ        TCGA-UZ-A9Q0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UZ-A9Q1        TCGA-WN-A9G9        TCGA-WN-AB4C        TCGA-Y8-A894 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A895        TCGA-Y8-A896        TCGA-Y8-A897        TCGA-Y8-A898 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Y8-A8RY        TCGA-Y8-A8RZ        TCGA-Y8-A8S0        TCGA-Y8-A8S1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   1
  2P LOSS WILD-TYPE  12 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    1
  2P LOSS WILD-TYPE   12  219
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               1               219
[1] 2 2
[1] FALSE

Clustering(44) Variable = 3P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    15   6
  3P LOSS WILD-TYPE 207  28
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21               235 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6                28 
$`3P LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3473 
       54.64        51.52        38.99         8.48        12.99        25.08 
TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5892 TCGA-DZ-6131 
        2.10        14.86         8.88        21.63        11.97        79.86 
TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
        4.01        17.33         3.68         2.04         0.13        14.07 
TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A8RZ 
       86.27        26.01         6.74 

$`3P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         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-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12        43.99        22.06        19.23         6.81         0.16 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        86.76        19.27        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       25.35        13.25        10.88         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        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        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        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         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       50.60        78.90        12.85        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93         0.53        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        25.68        27.39        12.99        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       15.91        18.64        18.05        15.62        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.13              0.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            86.27            194.79 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            14.07             21.93 
[1] "0.1 - 86.3 (14.1)"  "0.1 - 194.8 (21.9)"
[1] "hr=" "3"  
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         5        1        12        3
  3P LOSS WILD-TYPE     162       20        37       11
D44V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 5               162
  STAGE II                1                20
  STAGE III              12                37
  STAGE IV                3                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  3P LOSS MUTATED     6   3    12
  3P LOSS WILD-TYPE 170  26    44
D44V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  6               170
  T2                  3                26
  T3+T4              12                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  3P LOSS MUTATED    6  6  1
  3P LOSS WILD-TYPE 39 16  3
D44V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               6                39
  N1               6                16
  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"
D44V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    4  2
  3P LOSS WILD-TYPE 86  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    2
  3P LOSS WILD-TYPE   86    7
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               4                86
  1               2                 7
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     5  16
  3P LOSS WILD-TYPE  67 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5   16
  3P LOSS WILD-TYPE   67  181
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                67
  MALE                16               181
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
D44V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     1
  3P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           4    15
  3P LOSS WILD-TYPE                        56   172
D44V11, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      4                56
  WHITE                                         15               172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0  18
  3P LOSS WILD-TYPE  12 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   18
  3P LOSS WILD-TYPE   12  202
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              18               202
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     3   3
  3Q LOSS WILD-TYPE 219  31
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               250 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                31 
$`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        17.33         3.68 

$`3Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI 
        4.57        67.30        75.42        34.85        56.81        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
       14.86        17.49        12.30        86.76        19.27        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       13.68        25.84         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         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 
           13.105            21.555 
[1] "3.7 - 54.6 (13.1)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "6.6"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         2        0         2        2
  3Q LOSS WILD-TYPE     165       21        47       12
D45V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 2               165
  STAGE II                0                21
  STAGE III               2                47
  STAGE IV                2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  3Q LOSS MUTATED     2   0     4
  3Q LOSS WILD-TYPE 174  29    52
D45V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                  2               174
  T2                  0                29
  T3+T4               4                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
  3Q LOSS MUTATED    1  2  1
  3Q LOSS WILD-TYPE 44 20  3
D45V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               1                44
  N1               2                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"
D45V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  1
  3Q LOSS WILD-TYPE 89  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    1
  3Q LOSS WILD-TYPE   89    8
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               1                89
  1               1                 8
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2   4
  3Q LOSS WILD-TYPE  70 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    4
  3Q LOSS WILD-TYPE   70  193
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                70
  MALE                 4               193
[1] 2 2
[1] FALSE
D45V8, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                59 
       TCGA-2Z-A9JK        TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7286 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT        TCGA-A4-A57E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D45V9, continuous
D45V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1     4
  3Q LOSS WILD-TYPE                        59   183
D45V11, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                59
  WHITE                                          4               183
[1] 4 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
  3Q LOSS MUTATED     0   4
  3Q LOSS WILD-TYPE  12 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    4
  3Q LOSS WILD-TYPE   12  216
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               4               216
[1] 2 2
[1] FALSE

Clustering(46) Variable = 4P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    14   8
  4P LOSS WILD-TYPE 208  26
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               22               234 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                26 
$`4P LOSS MUTATED`
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7287 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 
       51.52        12.82        19.63        49.25         7.33        10.09 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       22.92        21.63         2.76        79.86        10.68        13.08 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 
       13.68        16.90         3.68        73.25         2.04         0.13 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       42.94         6.61        14.07        18.02 

$`4P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        18.21        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        6.58        33.83        30.58        34.49        12.46        10.16 
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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
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-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        8.88        63.72        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.92       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
       13.78         3.75        14.63         3.02        40.77        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        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        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
       11.05        39.25        34.82        25.15        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.98        17.33        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       68.12        13.41        11.84        56.75         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
       25.97        21.44        15.48        99.78        87.22        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            79.86            194.79 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           13.875            22.160 
[1] "0.1 - 79.9 (13.9)"  "0.1 - 194.8 (22.2)"
[1] "hr=" "4.6"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         4        1        15        1
  4P LOSS WILD-TYPE     163       20        34       13
D46V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 4               163
  STAGE II                1                20
  STAGE III              15                34
  STAGE IV                1                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   2    15
  4P LOSS WILD-TYPE 171  27    41
D46V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                  5               171
  T2                  2                27
  T3+T4              15                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
  4P LOSS MUTATED    3  9  0
  4P LOSS WILD-TYPE 42 13  4
D46V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0               3                42
  N1               9                13
  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"
D46V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    8  1
  4P LOSS WILD-TYPE 82  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8    1
  4P LOSS WILD-TYPE   82    8
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               8                82
  1               1                 8
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    15   8
  4P LOSS WILD-TYPE  57 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     15    8
  4P LOSS WILD-TYPE   57  189
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              15                57
  MALE                 8               189
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           5    12
  4P LOSS WILD-TYPE                        55   175
D46V11, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      5                55
  WHITE                                         12               175
[1] 4 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
  4P LOSS MUTATED     1  16
  4P LOSS WILD-TYPE  11 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   16
  4P LOSS WILD-TYPE   11  204
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              16               204
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    15   8
  4Q LOSS WILD-TYPE 207  26
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               23               233 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                8                26 
$`4Q LOSS MUTATED`
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7287 TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B1-7332 
       51.52        12.82        19.63         8.48        49.25         7.33 
TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ 
       10.09        19.27        21.63         2.76        79.86        10.68 
TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-A5NK TCGA-IA-A40Y 
       13.08        13.68        16.90         3.68        73.25         2.04 
TCGA-J7-8537 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 
        0.13        42.94         6.61        14.07        18.02 

$`4Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        18.21        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        12.30        86.76         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.92       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        40.77        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       61.02        54.90        34.19        19.00        24.89         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        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        34.82        25.15        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       17.33        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       13.41        11.84        56.75         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
       21.44        15.48        99.78        87.22        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.13              0.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            79.86            194.79 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            13.68             22.49 
[1] "0.1 - 79.9 (13.7)"  "0.1 - 194.8 (22.5)"
[1] "hr=" "4.6"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         5        1        14        2
  4Q LOSS WILD-TYPE     162       20        35       12
D47V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 5               162
  STAGE II                1                20
  STAGE III              14                35
  STAGE IV                2                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   3    14
  4Q LOSS WILD-TYPE 170  26    42
D47V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                  6               170
  T2                  3                26
  T3+T4              14                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
  4Q LOSS MUTATED    4  8  0
  4Q LOSS WILD-TYPE 41 14  4
D47V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0               4                41
  N1               8                14
  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"
D47V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    8  2
  4Q LOSS WILD-TYPE 82  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8    2
  4Q LOSS WILD-TYPE   82    7
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               8                82
  1               2                 7
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    14  10
  4Q LOSS WILD-TYPE  58 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     14   10
  4Q LOSS WILD-TYPE   58  187
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              14                58
  MALE                10               187
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           5    13
  4Q LOSS WILD-TYPE                        55   174
D47V11, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      5                55
  WHITE                                         13               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"
D47V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     1  17
  4Q LOSS WILD-TYPE  11 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   17
  4Q LOSS WILD-TYPE   11  203
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              17               203
[1] 2 2
[1] FALSE

Clustering(48) Variable = 5P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     3   5
  5P LOSS WILD-TYPE 219  29
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               248 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5                29 
$`5P 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-G7-6793 TCGA-P4-A5EA 
       11.05         6.61 

$`5P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        0.13        12.82        11.57        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 
       19.13         0.89         0.23        16.64        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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
       12.30        86.76        19.27         8.88        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.92       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 
       61.02        54.90        34.19        19.00        24.89        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        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       21.44        15.48        99.78        87.22        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
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 
            14.63             21.65 
[1] "2.8 - 30.5 (14.6)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "13" 
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         2        0         3        2
  5P LOSS WILD-TYPE     165       21        46       12
D48V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 2               165
  STAGE II                0                21
  STAGE III               3                46
  STAGE IV                2                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
  5P LOSS MUTATED     2   0     6
  5P LOSS WILD-TYPE 174  29    50
D48V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                  2               174
  T2                  0                29
  T3+T4               6                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
  5P LOSS MUTATED    0  3  1
  5P LOSS WILD-TYPE 45 19  3
D48V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0               0                45
  N1               3                19
  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
  5P LOSS MUTATED    2  1
  5P LOSS WILD-TYPE 88  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    1
  5P LOSS WILD-TYPE   88    8
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               2                88
  1               1                 8
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5   3
  5P LOSS WILD-TYPE  67 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    3
  5P LOSS WILD-TYPE   67  194
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                67
  MALE                 3               194
[1] 2 2
[1] FALSE
D48V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                58 
       TCGA-2Z-A9JK        TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7828 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8518 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466        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-DW-7963        TCGA-EV-5901        TCGA-EV-5902 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6796        TCGA-G7-6797 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537        TCGA-P4-AAVK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-SX-A7SU 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D48V9, continuous
D48V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1     6
  5P LOSS WILD-TYPE                        59   181
D48V11, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                59
  WHITE                                          6               181
[1] 4 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
  5P LOSS MUTATED     1   5
  5P LOSS WILD-TYPE  11 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    5
  5P LOSS WILD-TYPE   11  215
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               5               215
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     4   4
  5Q LOSS WILD-TYPE 218  30
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8               248 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                30 
$`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-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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        0.13        12.82        11.57        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 
       19.13         0.89         0.23        16.64        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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
       12.30        86.76        19.27         8.88        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.92       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 
       61.02        54.90        34.19        19.00        24.89        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        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
        6.38        17.98        17.33        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       21.44        15.48        99.78        87.22        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        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            21.650 
[1] "2.8 - 30.5 (14.4)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "11" 
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         2        0         4        1
  5Q LOSS WILD-TYPE     165       21        45       13
D49V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 2               165
  STAGE II                0                21
  STAGE III               4                45
  STAGE IV                1                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
  5Q LOSS MUTATED     2   0     6
  5Q LOSS WILD-TYPE 174  29    50
D49V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  2               174
  T2                  0                29
  T3+T4               6                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
  5Q LOSS MUTATED    0  4  0
  5Q LOSS WILD-TYPE 45 18  4
D49V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               0                45
  N1               4                18
  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"
D49V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2  1
  5Q LOSS WILD-TYPE 88  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    1
  5Q LOSS WILD-TYPE   88    8
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               2                88
  1               1                 8
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5   3
  5Q LOSS WILD-TYPE  67 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    3
  5Q LOSS WILD-TYPE   67  194
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               5                67
  MALE                 3               194
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                59 
       TCGA-2Z-A9JK        TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7828 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8518 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466        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-DW-7963        TCGA-EV-5901        TCGA-EV-5902 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D49V9, continuous
D49V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     0
  5Q LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1     6
  5Q LOSS WILD-TYPE                        59   181
D49V11, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                59
  WHITE                                          6               181
[1] 4 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
  5Q LOSS MUTATED     1   5
  5Q LOSS WILD-TYPE  11 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    5
  5Q LOSS WILD-TYPE   11  215
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               5               215
[1] 2 2
[1] FALSE

Clustering(50) Variable = 6P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    14   4
  6P LOSS WILD-TYPE 208  30
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               18               238 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4                30 
$`6P LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-5882 TCGA-BQ-7056 
       54.64        51.52        18.21        10.09        21.63        20.12 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7502 
       19.00        13.08         4.01        11.05        25.15        25.84 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-P4-A5E8 TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-Y8-A896 
       17.33         3.68        42.94        27.06        18.02        18.64 

$`6P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         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-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        24.89        10.68         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
        0.43        51.78        48.62        39.25        34.82        13.68 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
       14.07        47.90        47.44        33.04        28.80        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
       26.01        29.00        18.64        15.91        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             3.68              0.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            54.64            194.79 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            18.82             21.80 
[1] "3.7 - 54.6 (18.8)"  "0.1 - 194.8 (21.8)"
[1] "hr=" "2.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         8        0         8        2
  6P LOSS WILD-TYPE     159       21        41       12
D50V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 8               159
  STAGE II                0                21
  STAGE III               8                41
  STAGE IV                2                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 LOSS MUTATED     9   1     9
  6P LOSS WILD-TYPE 167  28    47
D50V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                  9               167
  T2                  1                28
  T3+T4               9                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
  6P LOSS MUTATED    3  2  2
  6P LOSS WILD-TYPE 42 20  2
D50V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0               3                42
  N1               2                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"
D50V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    8  0
  6P LOSS WILD-TYPE 82  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      8    0
  6P LOSS WILD-TYPE   82    9
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               8                82
  1               0                 9
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     8  11
  6P LOSS WILD-TYPE  64 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      8   11
  6P LOSS WILD-TYPE   64  186
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               8                64
  MALE                11               186
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
D50V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     1
  6P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           1    14
  6P LOSS WILD-TYPE                        59   173
D50V11, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      1                59
  WHITE                                         14               173
[1] 4 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
  6P LOSS MUTATED     0  15
  6P LOSS WILD-TYPE  12 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   15
  6P LOSS WILD-TYPE   12  205
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              15               205
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    20   3
  6Q LOSS WILD-TYPE 202  31
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               23               233 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                31 
$`6Q LOSS MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-A4-7286 TCGA-B3-3926 
       67.30        54.64        51.52        35.67        18.21        10.09 
TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5888 TCGA-BQ-7056 TCGA-EV-5902 
        2.10        86.76        21.63        13.25        20.12        19.00 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 
       13.08         4.01        11.05        25.84        17.33         3.68 
TCGA-J7-8537 TCGA-P4-A5EB TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-Y8-A896 
        0.13        84.95        27.06        18.02        18.64 

$`6Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL 
        4.57        75.42        34.85        56.81        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 
       16.18        22.49         0.13        12.82        11.57        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         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-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        6.58        33.83        30.58        34.49        12.46        10.16 
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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12        43.99        22.06        19.23         6.81         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-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        25.35        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       44.84        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       61.02        54.90        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        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       25.15        13.68         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
       12.99        26.01        29.00        18.64        15.91        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.13              0.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            86.76            194.79 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            18.64             21.93 
[1] "0.1 - 86.8 (18.6)"  "0.1 - 194.8 (21.9)"
[1] "hr=" "1"  
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED        12        0         9        2
  6Q LOSS WILD-TYPE     155       21        40       12
D51V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                12               155
  STAGE II                0                21
  STAGE III               9                40
  STAGE IV                2                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 LOSS MUTATED    12   0    12
  6Q LOSS WILD-TYPE 164  29    44
D51V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                 12               164
  T2                  0                29
  T3+T4              12                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  6Q LOSS MUTATED    4  2  2
  6Q LOSS WILD-TYPE 41 20  2
D51V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0               4                41
  N1               2                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"
D51V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   11  0
  6Q LOSS WILD-TYPE 79  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     11    0
  6Q LOSS WILD-TYPE   79    9
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              11                79
  1               0                 9
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    12  12
  6Q LOSS WILD-TYPE  60 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12   12
  6Q LOSS WILD-TYPE   60  185
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              12                60
  MALE                12               185
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
D51V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     2
  6Q LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           2    17
  6Q LOSS WILD-TYPE                        58   170
D51V11, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      2                58
  WHITE                                         17               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"
D51V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0  18
  6Q LOSS WILD-TYPE  12 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   18
  6Q LOSS WILD-TYPE   12  202
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              18               202
[1] 2 2
[1] FALSE

Clustering(52) Variable = 8P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED     8   5
  8P LOSS WILD-TYPE 214  29
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13               243 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                29 
$`8P LOSS MUTATED`
TCGA-2Z-A9J3 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5889 
       58.22        12.99         9.63         7.33        10.09        10.88 
TCGA-DW-5560 TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-A8LC TCGA-G7-A8LD TCGA-SX-A7SO 
       11.61        13.08         1.18        17.33        16.90        38.63 
TCGA-UN-AAZ9 
       18.02 

$`8P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        59.01       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       19.56        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        33.83        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         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-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.04         7.17         3.81        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
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        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
       25.15        13.68        25.84         6.38        17.98        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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        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         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        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-A9PK 
       16.31        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.18              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            58.22            194.79 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            12.99             22.06 
[1] "1.2 - 58.2 (13.0)"  "0.1 - 194.8 (22.1)"
[1] "hr=" "5.9"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         6        2         2        3
  8P LOSS WILD-TYPE     161       19        47       11
D52V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 6               161
  STAGE II                2                19
  STAGE III               2                47
  STAGE IV                3                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
  8P LOSS MUTATED     7   2     4
  8P LOSS WILD-TYPE 169  27    52
D52V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                  7               169
  T2                  2                27
  T3+T4               4                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
  8P LOSS MUTATED    1  5  0
  8P LOSS WILD-TYPE 44 17  4
D52V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0               1                44
  N1               5                17
  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"
D52V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4  3
  8P LOSS WILD-TYPE 86  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    3
  8P LOSS WILD-TYPE   86    6
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               4                86
  1               3                 6
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     6   7
  8P LOSS WILD-TYPE  66 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      6    7
  8P LOSS WILD-TYPE   66  190
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               6                66
  MALE                 7               190
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                63 
       TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-2Z-A9JD        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JQ        TCGA-4A-A93W 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4115        TCGA-B9-4117        TCGA-B9-7268        TCGA-B9-A44B 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7963 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A59T        TCGA-GL-A9DD        TCGA-HE-A5NI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U        TCGA-IA-A83S 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RY        TCGA-Y8-A8RZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D52V10, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                49 
       TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD        TCGA-2Z-A9JI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117        TCGA-B9-A69E 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-UZ-A9PR        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" 
       TCGA-Y8-A8RZ 
"8P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     2
  8P LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           2     9
  8P LOSS WILD-TYPE                        58   178
D52V11, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      2                58
  WHITE                                          9               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"
D52V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0  13
  8P LOSS WILD-TYPE  12 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   13
  8P LOSS WILD-TYPE   12  207
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              13               207
[1] 2 2
[1] FALSE

Clustering(53) Variable = 8Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     5   2
  8Q LOSS WILD-TYPE 217  32
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7               249 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                32 
$`8Q LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5889 TCGA-F9-A7Q0 TCGA-G7-A8LC 
       12.99         7.33        10.09        10.88        13.08        17.33 
TCGA-UN-AAZ9 
       18.02 

$`8Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       49.25         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
        3.55        16.77         0.46         6.58        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        25.35        13.25         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       10.68         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 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK 
       16.31        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             7.33              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            18.02            194.79 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            12.99             21.93 
[1] "7.3 - 18.0 (13.0)"  "0.1 - 194.8 (21.9)"
[1] "hr=" "5.8"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         4        1         1        1
  8Q LOSS WILD-TYPE     163       20        48       13
D53V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 4               163
  STAGE II                1                20
  STAGE III               1                48
  STAGE IV                1                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
  8Q LOSS MUTATED     5   1     1
  8Q LOSS WILD-TYPE 171  28    55
D53V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1                  5               171
  T2                  1                28
  T3+T4               1                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
  8Q LOSS MUTATED    1  2  0
  8Q LOSS WILD-TYPE 44 20  4
D53V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               1                44
  N1               2                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"
D53V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  1
  8Q LOSS WILD-TYPE 88  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    1
  8Q LOSS WILD-TYPE   88    8
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               2                88
  1               1                 8
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     4   3
  8Q LOSS WILD-TYPE  68 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4    3
  8Q LOSS WILD-TYPE   68  194
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               4                68
  MALE                 3               194
[1] 2 2
[1] FALSE
D53V8, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                59 
       TCGA-2Z-A9JK        TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7286 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT        TCGA-A4-A57E 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D53V9, continuous
D53V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2     4
  8Q LOSS WILD-TYPE                        58   183
D53V11, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      2                58
  WHITE                                          4               183
[1] 4 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
  8Q LOSS MUTATED     0   7
  8Q LOSS WILD-TYPE  12 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    7
  8Q LOSS WILD-TYPE   12  213
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               7               213
[1] 2 2
[1] FALSE

Clustering(54) Variable = 9P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    20  11
  9P LOSS WILD-TYPE 202  23
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               31               225 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11                23 
$`9P LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 
       54.64        51.52        35.67        12.82        18.21        19.63 
TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-4116 
        8.48        12.99         9.63        49.25        10.09        20.61 
TCGA-B9-A69E TCGA-BQ-5879 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7048 TCGA-BQ-7056 
       14.86        22.92        13.25        10.88        93.34        20.12 
TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 
       79.86        13.08         4.01        11.05        34.82        13.68 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       17.33        16.90         2.04         0.13        18.02        86.27 
TCGA-Y8-A896 
       18.64 

$`9P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK 
        4.57        67.30        75.42        34.85        56.81        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 
        5.29        16.18        22.49         0.13        11.57        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        33.83        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       10.16        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
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-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       30.28        26.04        25.35         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 
        7.92         2.76       123.62        48.26        96.92        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
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-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
        0.43        51.78        48.62        39.25        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
        6.38        17.98        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
        5.49        16.80        19.99        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
       22.26        21.34        16.34        12.36        11.97        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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR 
       43.76        60.03        14.83        21.93         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            93.34            194.79 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            17.33             22.49 
[1] "0.1 - 93.3 (17.3)"  "0.1 - 194.8 (22.5)"
[1] "hr=" "3.7"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         9        0        15        5
  9P LOSS WILD-TYPE     158       21        34        9
D54V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 9               158
  STAGE II                0                21
  STAGE III              15                34
  STAGE IV                5                 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    18
  9P LOSS WILD-TYPE 166  26    38
D54V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                 10               166
  T2                  3                26
  T3+T4              18                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
  9P LOSS MUTATED    6  9  2
  9P LOSS WILD-TYPE 39 13  2
D54V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               6                39
  N1               9                13
  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"
D54V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    9  3
  9P LOSS WILD-TYPE 81  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      9    3
  9P LOSS WILD-TYPE   81    6
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               9                81
  1               3                 6
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    16  16
  9P LOSS WILD-TYPE  56 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     16   16
  9P LOSS WILD-TYPE   56  181
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              16                56
  MALE                16               181
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
D54V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     2
  9P LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           4    25
  9P LOSS WILD-TYPE                        56   162
D54V11, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      4                56
  WHITE                                         25               162
[1] 4 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
  9P LOSS MUTATED     0  28
  9P LOSS WILD-TYPE  12 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   28
  9P LOSS WILD-TYPE   12  192
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              28               192
[1] 2 2
[1] FALSE

Clustering(55) Variable = 9Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    22   9
  9Q LOSS WILD-TYPE 200  25
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               31               225 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                9                25 
$`9Q LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 
       54.64        51.52        35.67        12.82        18.21        19.63 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-A44B 
       12.99         9.63        49.25        10.09        34.49         2.10 
TCGA-B9-A69E TCGA-BQ-5879 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7048 TCGA-BQ-7055 
       14.86        22.92        13.25        10.88        93.34        26.27 
TCGA-BQ-7056 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       20.12        79.86        10.68        13.08         4.01        11.05 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LC TCGA-IA-A40Y TCGA-J7-8537 TCGA-UN-AAZ9 
       34.82        13.68        17.33         2.04         0.13        18.02 
TCGA-Y8-A896 
       18.64 

$`9Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK 
        4.57        67.30        75.42        34.85        56.81        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 
        5.29        16.18        22.49         0.13        11.57        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
       16.77         0.46         6.58        33.83        30.58        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
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-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       30.28        26.04        25.35         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 
        7.92         2.76       123.62        48.26        96.92        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       61.28        50.40        49.84        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        80.88        51.19        61.02        54.90        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-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       48.62        39.25        25.15        25.84         6.38        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-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        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         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            93.34            194.79 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            17.33             22.26 
[1] "0.1 - 93.3 (17.3)"  "0.1 - 194.8 (22.3)"
[1] "hr=" "3.2"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED        10        1        15        4
  9Q LOSS WILD-TYPE     157       20        34       10
D55V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                10               157
  STAGE II                1                20
  STAGE III              15                34
  STAGE IV                4                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    11   1    19
  9Q LOSS WILD-TYPE 165  28    37
D55V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                 11               165
  T2                  1                28
  T3+T4              19                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  9Q LOSS MUTATED    5  7  2
  9Q LOSS WILD-TYPE 40 15  2
D55V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0               5                40
  N1               7                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"
D55V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   11  2
  9Q LOSS WILD-TYPE 79  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     11    2
  9Q LOSS WILD-TYPE   79    7
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              11                79
  1               2                 7
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    16  16
  9Q LOSS WILD-TYPE  56 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16   16
  9Q LOSS WILD-TYPE   56  181
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              16                56
  MALE                16               181
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
D55V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           4    25
  9Q LOSS WILD-TYPE                        56   162
D55V11, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      4                56
  WHITE                                         25               162
[1] 4 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
  9Q LOSS MUTATED     0  26
  9Q LOSS WILD-TYPE  12 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0   26
  9Q LOSS WILD-TYPE   12  194
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              26               194
[1] 2 2
[1] FALSE

Clustering(56) Variable = 10P LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    10   4
  10P LOSS WILD-TYPE 212  30
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                242 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 30 
$`10P LOSS MUTATED`
TCGA-2Z-A9J8 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B9-4116 TCGA-B9-A44B 
       67.30        12.99         9.63        49.25        20.61         2.10 
TCGA-BQ-5876 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
       19.27        79.86         4.01        13.68        25.84        17.33 
TCGA-GL-7966 TCGA-Q2-A5QZ 
        3.68        14.07 

$`10P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
        4.57        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       12.46        10.16        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        80.88        51.19        61.02        54.90        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        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.15         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               2.1                0.1 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             79.86             194.79 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              15.7               21.8 
[1] "2.1 - 79.9 (15.7)"  "0.1 - 194.8 (21.8)"
[1] "hr=" "2.9"
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         4        0         7        2
  10P LOSS WILD-TYPE     163       21        42       12
D56V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  4                163
  STAGE II                 0                 21
  STAGE III                7                 42
  STAGE IV                 2                 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
  10P LOSS MUTATED     5   1     8
  10P LOSS WILD-TYPE 171  28    48
D56V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                   5                171
  T2                   1                 28
  T3+T4                8                 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
  10P LOSS MUTATED    1  4  1
  10P LOSS WILD-TYPE 44 18  3
D56V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                1                 44
  N1                4                 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"
D56V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  1
  10P LOSS WILD-TYPE 89  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    1
  10P LOSS WILD-TYPE   89    8
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                1                 89
  1                1                  8
[1] 2 2
[1] FALSE
D56V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6   8
  10P LOSS WILD-TYPE  66 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    8
  10P LOSS WILD-TYPE   66  189
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                6                 66
  MALE                  8                189
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     0
  10P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           4    10
  10P LOSS WILD-TYPE                        56   177
D56V11, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       4                 56
  WHITE                                          10                177
[1] 4 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
  10P LOSS MUTATED     0  12
  10P LOSS WILD-TYPE  12 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0   12
  10P LOSS WILD-TYPE   12  208
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               12                208
[1] 2 2
[1] FALSE

Clustering(57) Variable = 10Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    10   5
  10Q LOSS WILD-TYPE 212  29
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                241 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 29 
$`10Q LOSS MUTATED`
TCGA-2Z-A9J8 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5876 
       67.30        12.99         9.63        49.25         2.10        19.27 
TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 
       79.86         4.01        13.68        25.84        17.33         3.68 
TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
        0.13        14.07        86.27 

$`10Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
        4.57        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
        0.46         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         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-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
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        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       34.82        25.15         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       21.93         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.13               0.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             86.27             194.79 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             14.07              21.67 
[1] "0.1 - 86.3 (14.1)"  "0.1 - 194.8 (21.7)"
[1] "hr=" "2.9"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         4        0         9        2
  10Q LOSS WILD-TYPE     163       21        40       12
D57V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  4                163
  STAGE II                 0                 21
  STAGE III                9                 40
  STAGE IV                 2                 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
  10Q LOSS MUTATED     5   1     9
  10Q LOSS WILD-TYPE 171  28    47
D57V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                   5                171
  T2                   1                 28
  T3+T4                9                 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
  10Q LOSS MUTATED    1  6  1
  10Q LOSS WILD-TYPE 44 16  3
D57V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                1                 44
  N1                6                 16
  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
  10Q LOSS MUTATED    2  1
  10Q LOSS WILD-TYPE 88  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2    1
  10Q LOSS WILD-TYPE   88    8
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                2                 88
  1                1                  8
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6   9
  10Q LOSS WILD-TYPE  66 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6    9
  10Q LOSS WILD-TYPE   66  188
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                6                 66
  MALE                  9                188
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
D57V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     1
  10Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           4    10
  10Q LOSS WILD-TYPE                        56   177
D57V11, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       4                 56
  WHITE                                          10                177
[1] 4 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
  10Q LOSS MUTATED     0  13
  10Q LOSS WILD-TYPE  12 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0   13
  10Q LOSS WILD-TYPE   12  207
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               13                207
[1] 2 2
[1] FALSE

Clustering(58) Variable = 11P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    10   5
  11P LOSS WILD-TYPE 212  29
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                241 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 29 
$`11P LOSS MUTATED`
TCGA-2Z-A9JG TCGA-4A-A93X TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B 
       54.64        12.82        19.63         7.33        34.49         2.10 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD 
       19.27         8.88        21.63         4.01        25.84        16.90 
TCGA-IA-A40Y TCGA-Y8-A896 TCGA-Y8-A8S1 
        2.04        18.64        13.28 

$`11P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI 
        4.57        67.30        75.42        34.85        56.81        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        18.21        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       19.56        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 
        0.46         6.58        33.83        10.09        30.58        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 
        0.16        14.86        17.49        12.30        86.76        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       13.68         6.38        17.98        17.33        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       18.64        15.91        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 
        6.02 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              2.04               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             54.64             194.79 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             16.90              22.06 
[1] "2.0 - 54.6 (16.9)"  "0.1 - 194.8 (22.1)"
[1] "hr=" "5.2"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         5        2         6        2
  11P LOSS WILD-TYPE     162       19        43       12
D58V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  5                162
  STAGE II                 2                 19
  STAGE III                6                 43
  STAGE IV                 2                 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     8
  11P LOSS WILD-TYPE 171  27    48
D58V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   5                171
  T2                   2                 27
  T3+T4                8                 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
  11P LOSS MUTATED    1  3  1
  11P LOSS WILD-TYPE 44 19  3
D58V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                1                 44
  N1                3                 19
  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
  11P LOSS MUTATED    4  1
  11P LOSS WILD-TYPE 86  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    1
  11P LOSS WILD-TYPE   86    8
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                4                 86
  1                1                  8
[1] 2 2
[1] FALSE
D58V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5  11
  11P LOSS WILD-TYPE  67 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5   11
  11P LOSS WILD-TYPE   67  186
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                5                 67
  MALE                 11                186
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 49 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         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-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         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-IA-A40U 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A8RY 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"11P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           3    11
  11P LOSS WILD-TYPE                        57   176
D58V11, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       3                 57
  WHITE                                          11                176
[1] 4 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
  11P LOSS MUTATED     0  12
  11P LOSS WILD-TYPE  12 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   12
  11P LOSS WILD-TYPE   12  208
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               12                208
[1] 2 2
[1] FALSE

Clustering(59) Variable = 11Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    13   6
  11Q LOSS WILD-TYPE 209  28
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                19                237 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                 28 
$`11Q LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5876 
       54.64        51.52        12.82         7.33         2.10        19.27 
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-F9-A97G 
        8.88        21.63        10.88         7.66       123.62         0.43 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-IA-A40Y TCGA-J7-8537 TCGA-UZ-A9PQ 
        4.01        11.05        25.84         2.04         0.13        86.27 
TCGA-Y8-A896 
       18.64 

$`11Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       19.56        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
        0.46         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 
       30.28        26.04        25.35        13.25         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.92         2.76        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       13.08         2.40         1.18        51.78        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       34.82        25.15        13.68         6.38        17.98        17.33 
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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        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         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR 
       18.02        60.03        14.83        21.93         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.13               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            123.62             194.79 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             11.05              22.06 
[1] "0.1 - 123.6 (11.1)" "0.1 - 194.8 (22.1)"
[1] "hr=" "3.1"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         3        1        11        4
  11Q LOSS WILD-TYPE     164       20        38       10
D59V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  3                164
  STAGE II                 1                 20
  STAGE III               11                 38
  STAGE IV                 4                 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    14
  11Q LOSS WILD-TYPE 173  27    42
D59V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   3                173
  T2                   2                 27
  T3+T4               14                 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
  11Q LOSS MUTATED    3  5  2
  11Q LOSS WILD-TYPE 42 17  2
D59V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                3                 42
  N1                5                 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"
D59V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    7  2
  11Q LOSS WILD-TYPE 83  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      7    2
  11Q LOSS WILD-TYPE   83    7
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                7                 83
  1                2                  7
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6  14
  11Q LOSS WILD-TYPE  66 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6   14
  11Q LOSS WILD-TYPE   66  183
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                6                 66
  MALE                 14                183
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
D59V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           4    12
  11Q LOSS WILD-TYPE                        56   175
D59V11, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       4                 56
  WHITE                                          12                175
[1] 4 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
  11Q LOSS MUTATED     0  15
  11Q LOSS WILD-TYPE  12 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   15
  11Q LOSS WILD-TYPE   12  205
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               15                205
[1] 2 2
[1] FALSE

Clustering(60) Variable = 13Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    14   9
  13Q LOSS WILD-TYPE 208  25
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                233 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 9                 25 
$`13Q LOSS MUTATED`
TCGA-2Z-A9JI TCGA-A4-7287 TCGA-A4-7915 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B3-A6W5 
       51.52        19.63         0.23        49.25        10.09        10.16 
TCGA-BQ-5875 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       86.76        22.92        21.63         2.76        10.68        13.08 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 
        4.01        11.05        25.84        17.33        16.90         3.68 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 
        2.04         0.13        42.94        14.07        18.02 

$`13Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        18.21        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
       19.13         0.89        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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        17.49        12.30        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.92       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
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        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
       34.82        25.15        13.68         6.38        17.98        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.13               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             86.76             194.79 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             14.07              22.26 
[1] "0.1 - 86.8 (14.1)"  "0.1 - 194.8 (22.3)"
[1] "hr=" "5.5"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         7        1        12        3
  13Q LOSS WILD-TYPE     160       20        37       11
D60V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  7                160
  STAGE II                 1                 20
  STAGE III               12                 37
  STAGE IV                 3                 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
  13Q LOSS MUTATED     7   2    14
  13Q LOSS WILD-TYPE 169  27    42
D60V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                   7                169
  T2                   2                 27
  T3+T4               14                 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
  13Q LOSS MUTATED    3  7  2
  13Q LOSS WILD-TYPE 42 15  2
D60V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                3                 42
  N1                7                 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"
D60V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    7  1
  13Q LOSS WILD-TYPE 83  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      7    1
  13Q LOSS WILD-TYPE   83    8
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                7                 83
  1                1                  8
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    15   8
  13Q LOSS WILD-TYPE  57 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     15    8
  13Q LOSS WILD-TYPE   57  189
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               15                 57
  MALE                  8                189
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     2
  13Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           5    14
  13Q LOSS WILD-TYPE                        55   173
D60V11, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       5                 55
  WHITE                                          14                173
[1] 4 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
  13Q LOSS MUTATED     1  18
  13Q LOSS WILD-TYPE  11 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   18
  13Q LOSS WILD-TYPE   11  202
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               18                202
[1] 2 2
[1] FALSE

Clustering(61) Variable = 14Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    34  10
  14Q LOSS WILD-TYPE 188  24
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                44                212 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                10                 24 
$`14Q LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       54.64        51.52        38.99        18.21        19.63         0.10 
TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       29.46        12.99         9.63        25.08        44.61        49.25 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 
        7.33        16.77        10.09        20.61         6.81        19.27 
TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-DZ-6132 
       30.28        13.25        10.88         2.76        79.86        80.88 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 
       10.68        13.08         4.01        11.05        34.82        13.68 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40U 
       25.84        17.33        16.90        27.65        73.25        16.80 
TCGA-IA-A40Y TCGA-MH-A854 TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 
        2.04         0.36         6.61        12.85        14.07        18.02 
TCGA-UZ-A9PN TCGA-WN-A9G9 
       21.93        26.01 

$`14Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       61.05        35.18        19.13         0.89         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-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       13.55        30.35         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
       16.87         3.55         0.46         6.58        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       19.23         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-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       40.83        26.04        26.04        25.35         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.92       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 
        3.75        14.63         3.02        40.77        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        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-A4TM 
        0.43        51.78        48.62        39.25        25.15         6.38 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM 
       17.98        80.65       194.79        12.92         3.68         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S 
       13.41        11.84        56.75         5.49        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       30.38        27.65        20.25        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        25.68        27.39        12.99        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        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 
            17.115             22.705 
[1] "0.1 - 80.9 (17.1)"  "0.1 - 194.8 (22.7)"
[1] "hr=" "2.9"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        18        3        14        6
  14Q LOSS WILD-TYPE     149       18        35        8
D61V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 18                149
  STAGE II                 3                 18
  STAGE III               14                 35
  STAGE IV                 6                  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
  14Q LOSS MUTATED    20   4    20
  14Q LOSS WILD-TYPE 156  25    36
D61V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                  20                156
  T2                   4                 25
  T3+T4               20                 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
  14Q LOSS MUTATED    8  8  3
  14Q LOSS WILD-TYPE 37 14  1
D61V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                8                 37
  N1                8                 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"
D61V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   12  3
  14Q LOSS WILD-TYPE 78  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12    3
  14Q LOSS WILD-TYPE   78    6
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               12                 78
  1                3                  6
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    19  25
  14Q LOSS WILD-TYPE  53 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     19   25
  14Q LOSS WILD-TYPE   53  172
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               19                 53
  MALE                 25                172
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
D61V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     1
  14Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          10    30
  14Q LOSS WILD-TYPE                        50   157
D61V11, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                      10                 50
  WHITE                                          30                157
[1] 4 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
  14Q LOSS MUTATED     1  37
  14Q LOSS WILD-TYPE  11 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   37
  14Q LOSS WILD-TYPE   11  183
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               37                183
[1] 2 2
[1] FALSE

Clustering(62) Variable = 15Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    21   7
  15Q LOSS WILD-TYPE 201  27
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                28                228 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 27 
$`15Q LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-A5Y1 
       54.64        51.52        12.82        18.21         0.10        12.99 
TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5889 
       19.56        10.09         6.81        22.92        21.63        10.88 
TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7502 
        2.76        10.68        13.08         4.01        34.82        25.84 
TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 TCGA-HE-A5NK TCGA-P4-A5EA TCGA-PJ-A5Z8 
       17.33       194.79         3.68        73.25         6.61        12.85 
TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-Y8-A896 TCGA-Y8-A8S1 
       18.02         0.53        18.64        13.28 

$`15Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05        35.18        19.13         0.89         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-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       44.61        49.25         2.20         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06         2.10        19.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
       12.30        86.76        19.27         8.88        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 
       13.25         7.66         0.95        11.97         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
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        48.62        11.05        39.25        25.15        13.68 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 
        6.38        17.98        16.90        80.65        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       68.12        13.41        11.84        56.75         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.22        42.94        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       50.60        78.90        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK 
       16.31        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       14.83        21.93        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.91        18.05        15.62        25.28         6.74         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 
            13.180             22.885 
[1] "0.1 - 194.8 (13.2)" "0.1 - 129.9 (22.9)"
[1] "hr=" "2.9"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED        11        1        10        4
  15Q LOSS WILD-TYPE     156       20        39       10
D62V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                 11                156
  STAGE II                 1                 20
  STAGE III               10                 39
  STAGE IV                 4                 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   1    14
  15Q LOSS WILD-TYPE 163  28    42
D62V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                  13                163
  T2                   1                 28
  T3+T4               14                 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
  15Q LOSS MUTATED    4  7  1
  15Q LOSS WILD-TYPE 41 15  3
D62V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                4                 41
  N1                7                 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"
D62V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   10  2
  15Q LOSS WILD-TYPE 80  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     10    2
  15Q LOSS WILD-TYPE   80    7
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               10                 80
  1                2                  7
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    10  19
  15Q LOSS WILD-TYPE  62 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     10   19
  15Q LOSS WILD-TYPE   62  178
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               10                 62
  MALE                 19                178
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 49 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4117 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-5561         TCGA-DW-7963 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-7501         TCGA-G7-A8LB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A8RY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"15Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     1
  15Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           4    20
  15Q LOSS WILD-TYPE                        56   167
D62V11, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       4                 56
  WHITE                                          20                167
[1] 4 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
  15Q LOSS MUTATED     1  23
  15Q LOSS WILD-TYPE  11 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   23
  15Q LOSS WILD-TYPE   11  197
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               23                197
[1] 2 2
[1] FALSE

Clustering(63) Variable = 16P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     0   3
  16P LOSS WILD-TYPE 222  31
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                253 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 31 
$`16P LOSS MUTATED`
TCGA-A4-7287 TCGA-BQ-5882 TCGA-G7-6793 
       19.63        21.63        11.05 

$`16P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 
        0.13        12.82        11.57        18.21        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         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-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        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-G7-6795 TCGA-G7-6796 
        0.43         4.01        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             11.05               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             21.63             194.79 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             19.63              21.44 
[1] "11.1 - 21.6 (19.6)" "0.1 - 194.8 (21.4)"
[1] "hr=" "14" 
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         1        0         2        1
  16P LOSS WILD-TYPE     166       21        47       13
D63V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                166
  STAGE II                 0                 21
  STAGE III                2                 47
  STAGE IV                 1                 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
  16P LOSS MUTATED     1   0     3
  16P LOSS WILD-TYPE 175  29    53
D63V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   1                175
  T2                   0                 29
  T3+T4                3                 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
  16P LOSS MUTATED    1  0  1
  16P LOSS WILD-TYPE 44 22  3
D63V5, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 69 
        TCGA-2Z-A9J1         TCGA-2Z-A9JO         TCGA-4A-A93W 
"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-A5Y1         TCGA-A4-A7UZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-3473 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-A47O 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B1-A657 
"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-5888         TCGA-BQ-5889 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-F9-A97G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6795         TCGA-G7-7501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-6846         TCGA-GL-7966 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A9DC         TCGA-IA-A40U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83W         TCGA-J7-6720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-J7-8537         TCGA-KV-A74V         TCGA-P4-A5E6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-SX-A71R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SP         TCGA-SX-A7SS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UN-AAZ9         TCGA-UZ-A9PM         TCGA-UZ-A9PQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-Y8-A897         TCGA-Y8-A8RZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D63V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  0
  16P LOSS WILD-TYPE 88  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    0
  16P LOSS WILD-TYPE   88    9
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                2                 88
  1                0                  9
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3   1
  16P LOSS WILD-TYPE  69 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    1
  16P LOSS WILD-TYPE   69  196
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 69
  MALE                  1                196
[1] 2 2
[1] FALSE
D63V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 59 
        TCGA-2Z-A9JK         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-A4-8310 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8630         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-5560         TCGA-DW-5561 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"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-G7-6790         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-A7SO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D63V9, continuous
D63V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           0     2
  16P LOSS WILD-TYPE                        60   185
D63V11, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                252 
        TCGA-2K-A9WE         TCGA-2Z-A9J1         TCGA-2Z-A9J2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J5         TCGA-2Z-A9J6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JE         TCGA-2Z-A9JG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JJ         TCGA-2Z-A9JK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JL         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-A9JQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JR         TCGA-2Z-A9JS         TCGA-2Z-A9JT 
"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-A4-7288         TCGA-A4-7583 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7584         TCGA-A4-7585         TCGA-A4-7732 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7828         TCGA-A4-7915 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7996         TCGA-A4-7997         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-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-8630         TCGA-A4-A48D 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A4ZT         TCGA-A4-A57E         TCGA-A4-A5DU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5XZ         TCGA-A4-A5Y0         TCGA-A4-A5Y1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A6HP         TCGA-A4-A772         TCGA-A4-A7UZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"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-AL-A5DJ         TCGA-AT-A5NU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B1-A47M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A47N         TCGA-B1-A47O         TCGA-B1-A654 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B1-A657 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-4104         TCGA-B3-8121         TCGA-B3-A6W5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A44B         TCGA-B9-A5W7         TCGA-B9-A5W8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-B9-A69E         TCGA-B9-A8YH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A8YI         TCGA-BQ-5875         TCGA-BQ-5876 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5883 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-7044         TCGA-BQ-7045 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"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-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6133         TCGA-DZ-6134 
"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-A59T         TCGA-GL-A9DC         TCGA-GL-A9DD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A9DE         TCGA-IA-A40U         TCGA-IA-A40X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83S         TCGA-IA-A83T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A83W         TCGA-IZ-8195         TCGA-IZ-8196 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IZ-A6M8         TCGA-IZ-A6M9         TCGA-J7-6720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-J7-8537         TCGA-KV-A6GD         TCGA-KV-A6GE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KV-A74V         TCGA-MH-A55W         TCGA-MH-A55Z 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A560         TCGA-MH-A561         TCGA-MH-A562 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A855         TCGA-MH-A856 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A857         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-PJ-A5Z8         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SM         TCGA-SX-A7SN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SO         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-A9PO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PP         TCGA-UZ-A9PQ         TCGA-UZ-A9PR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PU         TCGA-UZ-A9PV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-UZ-A9PZ         TCGA-UZ-A9Q0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9Q1         TCGA-WN-A9G9         TCGA-WN-AB4C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A895         TCGA-Y8-A896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A897         TCGA-Y8-A898         TCGA-Y8-A8RY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-Y8-A8S0         TCGA-Y8-A8S1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D63V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   2
  16P LOSS WILD-TYPE  12 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    2
  16P LOSS WILD-TYPE   12  218
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                2                218
[1] 2 2
[1] FALSE

Clustering(64) Variable = 16Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     1   5
  16Q LOSS WILD-TYPE 221  29
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                250 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 29 
$`16Q LOSS MUTATED`
TCGA-2Z-A9JI TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-BQ-5882 TCGA-G7-6793 TCGA-G7-A8LD 
       51.52        19.63        12.99        21.63        11.05        16.90 

$`16Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        18.21        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         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-3468 
       15.75         8.28        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         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-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        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-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        48.62        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        17.33        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             11.05               0.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             51.52             194.79 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            18.265             21.555 
[1] "11.1 - 51.5 (18.3)" "0.1 - 194.8 (21.6)"
[1] "hr=" "8.9"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         1        0         5        1
  16Q LOSS WILD-TYPE     166       21        44       13
D64V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                166
  STAGE II                 0                 21
  STAGE III                5                 44
  STAGE IV                 1                 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
  16Q LOSS MUTATED     2   0     5
  16Q LOSS WILD-TYPE 174  29    51
D64V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   2                174
  T2                   0                 29
  T3+T4                5                 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
  16Q LOSS MUTATED    1  2  1
  16Q LOSS WILD-TYPE 44 20  3
D64V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                1                 44
  N1                2                 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"
D64V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  0
  16Q LOSS WILD-TYPE 88  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    0
  16Q LOSS WILD-TYPE   88    9
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                2                 88
  1                0                  9
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3   4
  16Q LOSS WILD-TYPE  69 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    4
  16Q LOSS WILD-TYPE   69  193
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 69
  MALE                  4                193
[1] 2 2
[1] FALSE
D64V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 58 
        TCGA-2Z-A9JK         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-A4-8310 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8630         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-5560         TCGA-DW-5561 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6790         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-A7SO         TCGA-SX-A7SP 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SU 
"16Q LOSS WILD-TYPE" 
D64V9, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 63 
        TCGA-2Z-A9J2         TCGA-2Z-A9J5         TCGA-2Z-A9J7 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         TCGA-2Z-A9JK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JM         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JQ         TCGA-4A-A93W         TCGA-4A-A93Y 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-A48D         TCGA-A4-A57E 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3466         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-7268         TCGA-B9-A44B 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-5561         TCGA-DW-7834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-7501 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LE         TCGA-GL-7773 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-GL-A9DD         TCGA-HE-A5NI 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IZ-A6M8         TCGA-MH-A854 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E7         TCGA-P4-A5EB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-Y8-A894 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D64V10, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 49 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4117 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-5561         TCGA-DW-7963 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-7501         TCGA-G7-A8LB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-IA-A40U         TCGA-MH-A854 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E6         TCGA-P4-AAVK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"16Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           0     5
  16Q LOSS WILD-TYPE                        60   182
D64V11, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 60
  WHITE                                           5                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"
D64V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     0   5
  16Q LOSS WILD-TYPE  12 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    5
  16Q LOSS WILD-TYPE   12  215
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                5                215
[1] 2 2
[1] FALSE

Clustering(65) Variable = 17P LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     2   5
  17P LOSS WILD-TYPE 220  29
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                249 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                 29 
$`17P LOSS MUTATED`
TCGA-2Z-A9JI TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-A57E TCGA-AL-3466 TCGA-BQ-7058 
       51.52        19.63         0.23         8.48         9.63        11.28 
TCGA-G7-6793 
       11.05 

$`17P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        18.21        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
       19.13         0.89        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-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.99        12.46        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         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-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        20.12         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        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        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             51.52             194.79 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             11.05              21.67 
[1] "0.2 - 51.5 (11.1)"  "0.1 - 194.8 (21.7)"
[1] "hr=" "12" 
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         1        1         3        3
  17P LOSS WILD-TYPE     166       20        46       11
D65V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  1                166
  STAGE II                 1                 20
  STAGE III                3                 46
  STAGE IV                 3                 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
  17P LOSS MUTATED     1   2     5
  17P LOSS WILD-TYPE 175  27    51
D65V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                   1                175
  T2                   2                 27
  T3+T4                5                 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
  17P LOSS MUTATED    2  1  2
  17P LOSS WILD-TYPE 43 21  2
D65V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                2                 43
  N1                1                 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"
D65V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    2  2
  17P LOSS WILD-TYPE 88  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    2
  17P LOSS WILD-TYPE   88    7
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                2                 88
  1                2                  7
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4   4
  17P LOSS WILD-TYPE  68 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    4
  17P LOSS WILD-TYPE   68  193
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                4                 68
  MALE                  4                193
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
D65V10, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 49 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3472         TCGA-AL-7173 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4117         TCGA-B9-A69E 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7963         TCGA-F9-A97G 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-IA-A40U         TCGA-MH-A854 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E6         TCGA-P4-AAVK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"17P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     0
  17P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           1     6
  17P LOSS WILD-TYPE                        59   181
D65V11, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 59
  WHITE                                           6                181
[1] 4 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
  17P LOSS MUTATED     0   7
  17P LOSS WILD-TYPE  12 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0    7
  17P LOSS WILD-TYPE   12  213
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                7                213
[1] 2 2
[1] FALSE

Clustering(66) Variable = 18P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    26  12
  18P LOSS WILD-TYPE 196  22
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                38                218 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                 22 
$`18P LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JP TCGA-4A-A93X TCGA-A4-7286 
       54.64        51.52        35.67        29.36        12.82        18.21 
TCGA-A4-7287 TCGA-A4-8310 TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A656 
       19.63        25.64         8.48        49.25         7.33         0.46 
TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 
       10.09        20.61         8.88        22.92        21.63        25.35 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-DW-7840 
        2.76       123.62        93.34        11.28         7.63         3.75 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-GL-7773 TCGA-GL-7966 
       24.89        10.68        13.08         4.01        12.92         3.68 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A7SM 
        2.04         0.13         6.61        16.01        14.07        11.93 
TCGA-SX-A7SO TCGA-Y8-A8S1 
       38.63        13.28 

$`18P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK 
        4.57        67.30        75.42        34.85        56.81        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       26.43        30.71        24.33        31.20        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 
       16.18        22.49         0.13        11.57        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       29.46        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46        16.96        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 
       21.67        24.56        16.87         3.55        16.77         6.58 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
       17.49        12.30        86.76        19.27        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       47.80        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 
       10.88         7.66         0.95        11.97         7.92        48.26 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       20.12         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 
      129.86        35.93        37.55        24.46        13.78        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       54.90        34.19        19.00         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       13.68        25.84         6.38        17.98        17.33        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       80.65       194.79        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       52.27        50.60        78.90        12.85        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       47.44        33.04        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-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 
        6.74         6.02 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.13               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            123.62             194.79 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            13.180             22.885 
[1] "0.1 - 123.6 (13.2)" "0.1 - 194.8 (22.9)"
[1] "hr=" "4.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED        13        1        16        5
  18P LOSS WILD-TYPE     154       20        33        9
D66V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                 13                154
  STAGE II                 1                 20
  STAGE III               16                 33
  STAGE IV                 5                  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    13   3    21
  18P LOSS WILD-TYPE 163  26    35
D66V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                  13                163
  T2                   3                 26
  T3+T4               21                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18P LOSS MUTATED    5  8  2
  18P LOSS WILD-TYPE 40 14  2
D66V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                5                 40
  N1                8                 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"
D66V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   15  4
  18P LOSS WILD-TYPE 75  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     15    4
  18P LOSS WILD-TYPE   75    5
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               15                 75
  1                4                  5
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    16  23
  18P LOSS WILD-TYPE  56 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16   23
  18P LOSS WILD-TYPE   56  174
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               16                 56
  MALE                 23                174
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
D66V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     2
  18P LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           7    27
  18P LOSS WILD-TYPE                        53   160
D66V11, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       7                 53
  WHITE                                          27                160
[1] 4 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
  18P LOSS MUTATED     2  30
  18P LOSS WILD-TYPE  10 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   30
  18P LOSS WILD-TYPE   10  190
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               30                190
[1] 2 2
[1] FALSE

Clustering(67) Variable = 18Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    27  14
  18Q LOSS WILD-TYPE 195  20
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                41                215 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                14                 20 
$`18Q LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JP TCGA-4A-A93X TCGA-A4-7286 
       54.64        51.52        35.67        29.36        12.82        18.21 
TCGA-A4-7287 TCGA-A4-8310 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 
       19.63        25.64         8.48        12.99        49.25         7.33 
TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
        0.46        10.09        20.61         8.88        22.92        21.63 
TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7058 TCGA-BQ-7059 
       25.35         2.76       123.62        93.34        11.28         7.63 
TCGA-DW-7840 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 
        3.75        24.89        10.68        13.08         0.43         4.01 
TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA 
       16.90        12.92         3.68         2.04         0.13         6.61 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UZ-A9PQ TCGA-Y8-A8S1 
       14.07        11.93        38.63        86.27        13.28 

$`18Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK 
        4.57        67.30        75.42        34.85        56.81        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       26.43        30.71        24.33        31.20        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 
       16.18        22.49         0.13        11.57        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       29.46        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46        16.96        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        8.28        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 
       24.56        16.87         3.55        16.77         6.58        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       12.30        86.76        19.27        63.72        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 
        7.66         0.95        11.97         7.92        48.26        96.92 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
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        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 
        6.38        17.98        17.33        80.65       194.79        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        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         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        12.85        17.75        47.90        47.44        33.04 
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-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
        0.53        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.05        15.62        25.28         6.74         6.02 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.13               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            123.62             194.79 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             13.08              23.28 
[1] "0.1 - 123.6 (13.1)" "0.1 - 194.8 (23.3)"
[1] "hr=" "4.8"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED        13        1        20        5
  18Q LOSS WILD-TYPE     154       20        29        9
D67V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 13                154
  STAGE II                 1                 20
  STAGE III               20                 29
  STAGE IV                 5                  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    14   4    23
  18Q LOSS WILD-TYPE 162  25    33
D67V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                  14                162
  T2                   4                 25
  T3+T4               23                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18Q LOSS MUTATED    6 11  2
  18Q LOSS WILD-TYPE 39 11  2
D67V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                6                 39
  N1               11                 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"
D67V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   16  4
  18Q LOSS WILD-TYPE 74  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     16    4
  18Q LOSS WILD-TYPE   74    5
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               16                 74
  1                4                  5
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    16  26
  18Q LOSS WILD-TYPE  56 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     16   26
  18Q LOSS WILD-TYPE   56  171
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               16                 56
  MALE                 26                171
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
D67V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     3
  18Q LOSS WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           8    28
  18Q LOSS WILD-TYPE                        52   159
D67V11, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                  2
  BLACK OR AFRICAN AMERICAN                       8                 52
  WHITE                                          28                159
[1] 4 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
  18Q LOSS MUTATED     1  34
  18Q LOSS WILD-TYPE  11 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1   34
  18Q LOSS WILD-TYPE   11  186
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               34                186
[1] 2 2
[1] FALSE

Clustering(68) Variable = 19P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    12   3
  19P LOSS WILD-TYPE 210  31
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                15                241 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 31 
$`19P LOSS MUTATED`
TCGA-2Z-A9JG TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B9-A44B 
       54.64        18.21        25.64        12.99         7.33         2.10 
TCGA-BQ-5876 TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y 
       19.27         0.95         4.01        25.84        16.90         2.04 
TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-UZ-A9PN 
       84.95        14.07        21.93 

$`19P LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI 
        4.57        67.30        75.42        34.85        56.81        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
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-3468 TCGA-AL-3471 
        8.28        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        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        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        13.68         6.38        17.98        17.33        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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
        6.61        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.95               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             84.95             194.79 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             16.90              21.67 
[1] "0.9 - 85.0 (16.9)"  "0.1 - 194.8 (21.7)"
[1] "hr=" "2.4"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         4        1         8        1
  19P LOSS WILD-TYPE     163       20        41       13
D68V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  4                163
  STAGE II                 1                 20
  STAGE III                8                 41
  STAGE IV                 1                 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
  19P LOSS MUTATED     5   1     9
  19P LOSS WILD-TYPE 171  28    47
D68V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                   5                171
  T2                   1                 28
  T3+T4                9                 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
  19P LOSS MUTATED    1  3  1
  19P LOSS WILD-TYPE 44 19  3
D68V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                1                 44
  N1                3                 19
  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"
D68V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  0
  19P LOSS WILD-TYPE 88  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    0
  19P LOSS WILD-TYPE   88    9
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                2                 88
  1                0                  9
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     5  10
  19P LOSS WILD-TYPE  67 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      5   10
  19P LOSS WILD-TYPE   67  187
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                5                 67
  MALE                 10                187
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 49 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         TCGA-2Z-A9JN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LE         TCGA-GL-7773 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-PJ-A5Z9         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-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"19P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     0
  19P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           3    12
  19P LOSS WILD-TYPE                        57   175
D68V11, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       3                 57
  WHITE                                          12                175
[1] 4 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
  19P LOSS MUTATED     0  14
  19P LOSS WILD-TYPE  12 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   14
  19P LOSS WILD-TYPE   12  206
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               14                206
[1] 2 2
[1] FALSE

Clustering(69) Variable = 19Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    11   4
  19Q LOSS WILD-TYPE 211  30
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                241 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 30 
$`19Q LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A5Y1 TCGA-B1-7332 
       54.64        51.52        18.21        25.64        12.99         7.33 
TCGA-B9-A44B TCGA-BQ-5891 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD 
        2.10         0.95        10.68         4.01        25.84        16.90 
TCGA-IA-A40Y TCGA-Q2-A5QZ TCGA-UZ-A9PN 
        2.04        14.07        21.93 

$`19Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 
        0.89         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-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       25.08        44.61        49.25         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12        43.99        22.06        19.23         6.81         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        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-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       13.68         6.38        17.98        17.33        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       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 
             14.07              21.67 
[1] "0.9 - 54.6 (14.1)"  "0.1 - 194.8 (21.7)"
[1] "hr=" "3.6"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         2        1        10        1
  19Q LOSS WILD-TYPE     165       20        39       13
D69V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  2                165
  STAGE II                 1                 20
  STAGE III               10                 39
  STAGE IV                 1                 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
  19Q LOSS MUTATED     3   1    11
  19Q LOSS WILD-TYPE 173  28    45
D69V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                   3                173
  T2                   1                 28
  T3+T4               11                 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
  19Q LOSS MUTATED    1  3  1
  19Q LOSS WILD-TYPE 44 19  3
D69V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                1                 44
  N1                3                 19
  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
  19Q LOSS MUTATED    1  0
  19Q LOSS WILD-TYPE 89  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    0
  19Q LOSS WILD-TYPE   89    9
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                1                 89
  1                0                  9
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     6   9
  19Q LOSS WILD-TYPE  66 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    9
  19Q LOSS WILD-TYPE   66  188
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                6                 66
  MALE                  9                188
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
D69V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     0
  19Q LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           4    11
  19Q LOSS WILD-TYPE                        56   176
D69V11, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       4                 56
  WHITE                                          11                176
[1] 4 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
  19Q LOSS MUTATED     0  14
  19Q LOSS WILD-TYPE  12 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   14
  19Q LOSS WILD-TYPE   12  206
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               14                206
[1] 2 2
[1] FALSE

Clustering(70) Variable = 21Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    35   4
  21Q LOSS WILD-TYPE 187  30
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                39                217 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                 30 
$`21Q LOSS MUTATED`
TCGA-2Z-A9J6 TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JT TCGA-4A-A93X TCGA-A4-7288 
       56.91        51.52        30.71        22.49        12.82        61.05 
TCGA-A4-8516 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3468 
        0.76        16.96         8.48        16.31        15.75        76.64 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-4114 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       33.83        10.09        28.18         2.10        19.23         6.81 
TCGA-BQ-5875 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7061 
       86.76        30.28        10.88         7.66         2.76         7.17 
TCGA-DZ-6134 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-GL-7966 
       61.02        10.68        13.08         4.01        34.82         3.68 
TCGA-GL-A9DC TCGA-HE-A5NF TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GE TCGA-KV-A74V 
        0.89        68.12        16.80         2.04        29.10        11.41 
TCGA-PJ-A5Z9 TCGA-UZ-A9PN TCGA-UZ-A9PP 
       17.75        21.93         0.53 

$`21Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JJ 
       67.30        75.42        34.85        56.81        54.64        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       38.99        26.43        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
        5.29        16.18         0.13        11.57        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y1 
       19.63        19.73        14.33        12.46         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        58.45        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4115 
       30.58        34.49        12.46        10.16        50.50        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        17.49        12.30        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        26.04        25.35        13.25         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.92       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.04         3.81        11.61        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-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.02        40.77        79.86        80.88        51.19        54.90 
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        48.62        11.05        39.25        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       11.21         4.60        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
        5.49        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A55W 
       21.34        16.34        12.36         0.13        11.97        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        12.85        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       14.83        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.53               0.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             86.76             194.79 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             16.31              22.26 
[1] "0.5 - 86.8 (16.3)"  "0.1 - 194.8 (22.3)"
[1] "hr=" "1"  
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        17        3        14        4
  21Q LOSS WILD-TYPE     150       18        35       10
D70V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 17                150
  STAGE II                 3                 18
  STAGE III               14                 35
  STAGE IV                 4                 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   5    17
  21Q LOSS WILD-TYPE 158  24    39
D70V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                  18                158
  T2                   5                 24
  T3+T4               17                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  21Q LOSS MUTATED    6  5  1
  21Q LOSS WILD-TYPE 39 17  3
D70V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                6                 39
  N1                5                 17
  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
  21Q LOSS MUTATED   11  3
  21Q LOSS WILD-TYPE 79  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     11    3
  21Q LOSS WILD-TYPE   79    6
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               11                 79
  1                3                  6
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    15  26
  21Q LOSS WILD-TYPE  57 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     15   26
  21Q LOSS WILD-TYPE   57  171
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               15                 57
  MALE                 26                171
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
D70V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     1
  21Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           5    32
  21Q LOSS WILD-TYPE                        55   155
D70V11, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       5                 55
  WHITE                                          32                155
[1] 4 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
  21Q LOSS MUTATED     1  34
  21Q LOSS WILD-TYPE  11 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   34
  21Q LOSS WILD-TYPE   11  186
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               34                186
[1] 2 2
[1] FALSE

Clustering(71) Variable = 22Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    46  11
  22Q LOSS WILD-TYPE 176  23
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                199 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                11                 23 
$`22Q LOSS MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-8098 
       54.64        51.52        12.82        18.21        61.05        29.46 
TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B1-7332 
       19.63         8.28        12.99         9.63        49.25         7.33 
TCGA-B1-A47O TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 
       16.87        33.83        10.09         2.10         6.81        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-7055 TCGA-BQ-7056 
        2.76       123.62        61.28        50.40        26.27        20.12 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY 
        7.17        79.86        19.00        10.68        13.08         1.18 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
        4.01        11.05        25.15        13.68        25.84        17.33 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-MH-A856 TCGA-P4-A5EA TCGA-P4-AAVO 
        3.68         2.04         0.13        25.97         6.61        78.90 
TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-SX-A7SM TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ 
       14.07        27.06        11.93        18.02        21.93        86.27 
TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A8RZ 
       29.00        18.64         6.74 

$`22Q LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         0.89         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-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
        0.76        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       16.31        15.75        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-4103 
       24.56         3.55        16.77         0.46         6.58        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
       19.23         0.16        14.86        17.49        12.30        19.27 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5886 
       63.72        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 
       25.35        13.25        10.88        11.97         7.92        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7059 
       96.92        93.34        44.84        49.84        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.04         3.81        11.61        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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       24.89         2.40         0.43        51.78        48.62        39.25 
TCGA-G7-6796 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       34.82         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
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-A855 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
       20.25         0.36        12.13        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.22        42.94        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        12.85        17.75        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       28.80        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PR 
       48.30        43.76        60.03        14.83         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        15.91        18.05        15.62        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.13               0.10 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            123.62             194.79 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             18.02              22.49 
[1] "0.1 - 123.6 (18.0)" "0.1 - 194.8 (22.5)"
[1] "hr=" "2"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED        19        3        24        7
  22Q LOSS WILD-TYPE     148       18        25        7
D71V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 19                148
  STAGE II                 3                 18
  STAGE III               24                 25
  STAGE IV                 7                  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    22   4    29
  22Q LOSS WILD-TYPE 154  25    27
D71V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                  22                154
  T2                   4                 25
  T3+T4               29                 27
[1] 3 2
[1] 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   10 13  2
  22Q LOSS WILD-TYPE 35  9  2
D71V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               10                 35
  N1               13                  9
  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
  22Q LOSS MUTATED   20  5
  22Q LOSS WILD-TYPE 70  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     20    5
  22Q LOSS WILD-TYPE   70    4
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               20                 70
  1                5                  4
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    26  31
  22Q LOSS WILD-TYPE  46 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     26   31
  22Q LOSS WILD-TYPE   46  166
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               26                 46
  MALE                 31                166
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, continuous
D71V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0     3
  22Q LOSS WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          12    40
  22Q LOSS WILD-TYPE                        48   147
D71V11, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                  2
  BLACK OR AFRICAN AMERICAN                      12                 48
  WHITE                                          40                147
[1] 4 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
  22Q LOSS MUTATED     3  42
  22Q LOSS WILD-TYPE   9 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   42
  22Q LOSS WILD-TYPE    9  178
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               42                178
[1] 2 2
[1] FALSE

Clustering(72) Variable = XP LOSS MUTATION ANALYSIS
D72V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    20  10
  XP LOSS WILD-TYPE 202  24
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               30               226 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               10                24 
$`XP LOSS MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 
       67.30        54.64        51.52        12.82        18.21        19.63 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-5155 
       12.99         9.63         7.33        10.09        20.61        15.12 
TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 
        2.10        19.27         8.88        22.92        21.63        25.35 
TCGA-DW-5561 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6793 
       13.61        79.86        10.68        13.08         0.43        11.05 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       13.68        16.90         0.13        14.07        18.02        86.27 

$`XP LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK 
        4.57        75.42        34.85        56.81        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 
        5.29        16.18        22.49         0.13        11.57        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       76.64        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        2.20        19.56        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       12.46        10.16        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1.15        43.99        22.06        19.23         6.81         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-5886 TCGA-BQ-5888 
       47.80        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
        7.04         7.17         3.81        11.61       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-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        80.88        51.19        61.02        54.90        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 
       48.62        39.25        34.82        25.15        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        17.33        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
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-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR 
       43.76        60.03        14.83        21.93         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.13              0.10 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            86.27            194.79 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           14.595            23.295 
[1] "0.1 - 86.3 (14.6)"  "0.1 - 194.8 (23.3)"
[1] "hr=" "4"  
D72V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED         8        1        15        3
  XP LOSS WILD-TYPE     159       20        34       11
D72V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 8               159
  STAGE II                1                20
  STAGE III              15                34
  STAGE IV                3                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     9   3    17
  XP LOSS WILD-TYPE 167  26    39
D72V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T1                  9               167
  T2                  3                26
  T3+T4              17                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  XP LOSS MUTATED    5  8  1
  XP LOSS WILD-TYPE 40 14  3
D72V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0               5                40
  N1               8                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"
D72V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    9  2
  XP LOSS WILD-TYPE 81  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      9    2
  XP LOSS WILD-TYPE   81    7
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0               9                81
  1               2                 7
[1] 2 2
[1] FALSE
D72V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    12  18
  XP LOSS WILD-TYPE  60 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     12   18
  XP LOSS WILD-TYPE   60  179
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              12                60
  MALE                18               179
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, continuous
D72V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     3
  XP LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          10    16
  XP LOSS WILD-TYPE                        50   171
D72V11, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 2
  BLACK OR AFRICAN AMERICAN                     10                50
  WHITE                                         16               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"
D72V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0  23
  XP LOSS WILD-TYPE  12 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   23
  XP LOSS WILD-TYPE   12  197
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              23               197
[1] 2 2
[1] FALSE

Clustering(73) Variable = XQ LOSS MUTATION ANALYSIS
D73V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    17  10
  XQ LOSS WILD-TYPE 205  24
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               27               229 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               10                24 
$`XQ LOSS MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 
       67.30        54.64        51.52        12.82        18.21        19.63 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-5155 TCGA-BQ-5876 
       12.99         9.63         7.33        10.09        15.12        19.27 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-DW-5561 TCGA-DZ-6131 TCGA-F9-A4JJ 
        8.88        22.92        21.63        13.61        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        13.68        16.90         0.13 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       14.07        18.02        86.27 

$`XQ LOSS WILD-TYPE`
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK 
        4.57        75.42        34.85        56.81        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 
        5.29        16.18        22.49         0.13        11.57        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       76.64        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        2.20        19.56        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        0.46         1.15        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        40.77        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       61.02        54.90        34.19        19.00        24.89         2.40 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        1.18         4.01        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        25.84         6.38        17.98        17.33        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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        12.85        17.75        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        26.47        48.30        43.76        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       21.93         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.13              0.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            86.27            194.79 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            14.07             23.28 
[1] "0.1 - 86.3 (14.1)"  "0.1 - 194.8 (23.3)"
[1] "hr=" "4.4"
D73V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         8        1        13        3
  XQ LOSS WILD-TYPE     159       20        36       11
D73V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 8               159
  STAGE II                1                20
  STAGE III              13                36
  STAGE IV                3                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   2    15
  XQ LOSS WILD-TYPE 167  27    41
D73V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                  9               167
  T2                  2                27
  T3+T4              15                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
  XQ LOSS MUTATED    4  8  1
  XQ LOSS WILD-TYPE 41 14  3
D73V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0               4                41
  N1               8                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"
D73V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    8  2
  XQ LOSS WILD-TYPE 82  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8    2
  XQ LOSS WILD-TYPE   82    7
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               8                82
  1               2                 7
[1] 2 2
[1] FALSE
D73V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    11  16
  XQ LOSS WILD-TYPE  61 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11   16
  XQ LOSS WILD-TYPE   61  181
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              11                61
  MALE                16               181
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, continuous
D73V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     3
  XQ LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           8    15
  XQ LOSS WILD-TYPE                        52   172
D73V11, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 2
  BLACK OR AFRICAN AMERICAN                      8                52
  WHITE                                         15               172
[1] 4 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
  XQ LOSS MUTATED     0  21
  XQ LOSS WILD-TYPE  12 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   21
  XQ LOSS WILD-TYPE   12  199
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              21               199
[1] 2 2
[1] FALSE
