[1] "ofn"        "-oTKIRC-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/KIRC-TP/19775258/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/19781827/transformed.cor.cli.txt"

nPatients in clinical file=537, in cluster file=528, common to both=528
[1]  82 528
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24               504 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24               504 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               51               477 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               51               477 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               77               451 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               77               451 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               79               449 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               79               449 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               509 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               509 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               61               467 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               61               467 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               515 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               515 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               515 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               515 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              193               335 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              193               335 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              207               321 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              207               321 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11               517 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11               517 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               519 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               519 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              171               357 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              171               357 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              172               356 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              172               356 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               31               497 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               31               497 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               62               466 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               62               466 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               515 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               515 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               516 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               516 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                511 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                511 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                516 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                516 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                497 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                497 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                499 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                499 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               121                407 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               121                407 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               122                406 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               122                406 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                506 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                506 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                512 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                512 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                502 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                502 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               107                421 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               107                421 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                99                429 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                99                429 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                26                502 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                26                502 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                33                495 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                33                495 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                503 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                503 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                25                503 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                25                503 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                51                477 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                51                477 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                471 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                471 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               112                416 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               112                416 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               115                413 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               115                413 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                50                478 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                50                478 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                40                488 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                40                488 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               32               496 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               32               496 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               31               497 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               31               497 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               57               471 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               57               471 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               36               492 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               36               492 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               514 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               514 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               514 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               514 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              380               148 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              380               148 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               99               429 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               99               429 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72               456 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72               456 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65               463 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65               463 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               521 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               521 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               522 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               522 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              100               428 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              100               428 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              128               400 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              128               400 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               525 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               525 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               524 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               524 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              137               391 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              137               391 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               64               464 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               64               464 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              149               379 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              149               379 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              150               378 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              150               378 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                67                461 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                67                461 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                89                439 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                89                439 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                510 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                510 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                505 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                505 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                524 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                524 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                524 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                524 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                71                457 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                71                457 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               216                312 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               216                312 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                36                492 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                36                492 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                518 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                518 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                512 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                512 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                482 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                482 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                28                500 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                28                500 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                93                435 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                93                435 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                95                433 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                95                433 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                517 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                517 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                524 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                524 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                520 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                520 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                525 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                525 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                55                473 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                55                473 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                489 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                489 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               46               482 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               46               482 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               46               482 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               46               482 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 528 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=165,	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=357,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "134"   "2"    
freq.contrast "2"     "134"  
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 528 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
268  69 180  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
268  69 180  11 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
268  69 180  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
268  69 180  11 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=13, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    10  14
  1P GAIN WILD-TYPE 341 161
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24               502 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               14               161 
$`1P GAIN MUTATED`
TCGA-A3-3316 TCGA-A3-3372 TCGA-AK-3430 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-4838 
       49.08        24.16        15.78        22.45        52.21        27.42 
TCGA-B0-5092 TCGA-B0-5109 TCGA-B8-4143 TCGA-B8-5551 TCGA-BP-4352 TCGA-BP-4756 
       15.09        19.30        23.31         0.53        11.31        12.30 
TCGA-BP-4771 TCGA-BP-4974 TCGA-BP-5175 TCGA-CJ-4635 TCGA-CJ-4873 TCGA-CJ-5679 
        5.33         6.90        30.64        46.55        74.27        22.32 
TCGA-CJ-6027 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-5452 TCGA-MM-A564 
      118.85        83.90        18.77        69.21        58.82        19.96 

$`1P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
      109.91        29.10       117.80        73.08       109.41        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
      112.08        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       78.64        40.01        49.28        94.29        83.21        28.73 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       40.70        45.30        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        18.51        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        58.59        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       12.23        31.89        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68        10.82        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       74.20        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61       105.37        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       49.25        79.66        10.72        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 
      103.43        25.45        46.16         0.59        47.08        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       61.41        63.42        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       53.46        12.00        81.21        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        23.01        16.37        11.70 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.53              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           118.85            149.16 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           22.880            38.845 
[1] "0.5 - 118.8 (22.9)" "0.1 - 149.2 (38.8)"
[1] "hr=" "2.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         7        4         8        5
  1P GAIN WILD-TYPE     256       53       117       78
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 7               256
  STAGE II                4                53
  STAGE III               8               117
  STAGE IV                5                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     8   4  12   0
  1P GAIN WILD-TYPE 260  65 168  11
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               8               260
  T2               4                65
  T3              12               168
  T4               0                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"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    10   2
  1P GAIN WILD-TYPE 224  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     10    2
  1P GAIN WILD-TYPE  224   15
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              10               224
  1               2                15
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    18   5
  1P GAIN WILD-TYPE 400  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     18    5
  1P GAIN WILD-TYPE  400   73
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              18               400
  1               5                73
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8  16
  1P GAIN WILD-TYPE 181 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8   16
  1P GAIN WILD-TYPE  181  323
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               8               181
  MALE                16               323
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         2    21
  1P GAIN WILD-TYPE     7                        54   436
D1V11, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                54
  WHITE                                  21               436
[1] 3 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     1  15
  1P GAIN WILD-TYPE  25 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   15
  1P GAIN WILD-TYPE   25  335
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              15               335
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    27  24
  1Q GAIN WILD-TYPE 324 151
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               51               475 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24               151 
$`1Q GAIN MUTATED`
TCGA-A3-3316 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3430 
       49.08        34.29        31.07        24.16        18.87        15.78 
TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4713 TCGA-B0-4815 TCGA-B0-4838 TCGA-B0-4848 
       49.28        22.45         6.64        52.21        27.42        29.03 
TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5109 TCGA-B0-5115 TCGA-B0-5701 TCGA-B4-5843 
       15.09         2.24        19.30        52.73        80.91         0.36 
TCGA-B8-4143 TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4331 
       23.31         0.53        90.28        61.78        64.27        80.68 
TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4974 
       74.17        11.31        12.30         5.33        68.38         6.90 
TCGA-BP-5173 TCGA-BP-5175 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4873 TCGA-CJ-4876 
        1.74        30.64        46.55       114.41        74.27        64.27 
TCGA-CJ-4881 TCGA-CJ-4916 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 
       66.21        45.14        18.81       129.40        18.87        22.32 
TCGA-CJ-6027 TCGA-CW-5587 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4858 
      118.85        73.18        83.90        18.77        46.16        69.21 
TCGA-CZ-5452 TCGA-G6-A5PC TCGA-MM-A564 
       58.82         7.96        19.96 

$`1Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 
       38.99        38.47        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       94.19        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       83.21        28.73        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       12.13        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        2.53         3.48        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
       43.96         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
        5.52        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       68.71        40.70        45.30        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 
       10.52        10.29        65.29        39.45        26.07         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5097 
        7.30        25.32        18.51        10.95         8.05        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5117 
       30.48        58.59        66.05        38.63        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
      111.52       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       119.38       126.28        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        31.66        24.82        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         5.46         0.23        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       94.72       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 
       89.36        23.05        77.03        62.24        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       53.42         3.58        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       15.16         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       33.99        31.33        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
       10.82        61.97        60.59        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       79.30        74.20        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        63.25        73.22        14.17       106.16 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61       105.37        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 
       49.25        79.66        10.72        75.06       116.84        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 
       38.56         3.06         4.57       131.08        72.00       133.71 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 
       66.31        78.18        74.66         1.35       105.93       103.43 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
       25.45         0.59        47.08        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
      107.54        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
       81.21        18.12         3.91         6.77         4.18        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
       70.13        35.87         2.01        19.43        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.36              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.40            149.16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            31.07             38.56 
[1] "0.4 - 129.4 (31.1)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.5"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED        17        9        16        9
  1Q GAIN WILD-TYPE     246       48       109       74
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                17               246
  STAGE II                9                48
  STAGE III              16               109
  STAGE IV                9                74
[1] 4 2
[1] TRUE
[1] "dimension of 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    19  11  21   0
  1Q GAIN WILD-TYPE 249  58 159  11
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              19               249
  T2              11                58
  T3              21               159
  T4               0                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"
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    24   3
  1Q GAIN WILD-TYPE 210  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     24    3
  1Q GAIN WILD-TYPE  210   14
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              24               210
  1               3                14
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    41   9
  1Q GAIN WILD-TYPE 377  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     41    9
  1Q GAIN WILD-TYPE  377   69
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              41               377
  1               9                69
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    16  35
  1Q GAIN WILD-TYPE 173 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     16   35
  1Q GAIN WILD-TYPE  173  304
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              16               173
  MALE                35               304
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                20 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4VX 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-MM-A563        TCGA-T7-A92I 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
D2V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         4    46
  1Q GAIN WILD-TYPE     7                        52   411
D2V11, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               4                52
  WHITE                                  46               411
[1] 3 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     3  33
  1Q GAIN WILD-TYPE  23 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3   33
  1Q GAIN WILD-TYPE   23  317
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                23
  NOT HISPANIC OR LATINO              33               317
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    54  23
  2P GAIN WILD-TYPE 297 152
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               77               449 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               23               152 
$`2P GAIN MUTATED`
TCGA-3Z-A93Z TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3429 TCGA-AK-3430 
       12.66        24.16        18.87         0.10       109.41        15.78 
TCGA-AK-3444 TCGA-AK-3450 TCGA-B0-4690 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4811 
       48.36        49.28         1.41        19.73        57.70        46.59 
TCGA-B0-4813 TCGA-B0-5099 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5702 TCGA-B4-5832 
        0.59        15.95        19.30        38.63        71.41         5.10 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-5550 
        5.46         0.36        25.55        23.74         6.38        48.53 
TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4337 
        0.53         4.93       101.06         0.43        61.78         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4756 
       93.99        18.48        74.17        44.94        31.89        12.30 
TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4799 
       41.75        48.07        13.15        60.59        68.38        37.25 
TCGA-BP-4804 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-5173 TCGA-BP-5178 
       47.97        58.98        31.30         3.88         1.74        62.86 
TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4876 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 
       37.22        34.95        64.27        24.66       109.84        47.67 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5682 
       51.25        49.28       131.08        72.00       133.71       122.83 
TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 
       53.42       119.64        73.18        66.31        74.66        46.16 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 
       69.21        58.75         6.77        79.63        90.54        94.45 
TCGA-CZ-5461 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-A4VX TCGA-EU-5905 
       10.85        31.10        67.96        53.46         3.91 

$`2P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       11.90        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.64        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
       22.65         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      117.80        73.08        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        40.01        94.29        83.21 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         3.32         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       30.48        58.59        66.05        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
      111.52       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
       85.78        86.47       119.38       126.28        80.91        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        31.66        24.82        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         5.75         0.85         0.53         4.64 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 
       45.37        17.19        25.91        50.14        20.91         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 
       27.02         0.85        24.23        50.14        16.60        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 
       94.72        90.28        93.34        32.61        99.85        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       21.21        15.16        52.24        62.86        54.77        49.08 
TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       12.23        11.31        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4769 
       77.98        77.62         5.98        44.15        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
       10.82         5.33        61.97        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95        27.22        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10         6.35        79.30        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 
       13.41        24.62        33.47        19.82        44.55        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06       116.84        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       26.93        50.01        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       49.97       108.56        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5677 
       45.14         3.06         4.57        18.81       129.40        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        22.32        25.25        18.15        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 
       67.00        53.26       118.85        75.58        62.66         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5589 
       64.57        92.02        81.83         5.39        85.78        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
        0.59        47.08        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       18.44        91.69        55.33        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        22.52         2.40         1.94        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       56.84        23.90        12.00        81.21        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           133.71            149.16 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            46.16             37.58 
[1] "0.1 - 133.7 (46.2)" "0.1 - 149.2 (37.6)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        33        9        25       10
  2P GAIN WILD-TYPE     230       48       100       73
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                33               230
  STAGE II                9                48
  STAGE III              25               100
  STAGE IV               10                73
[1] 4 2
[1] TRUE
[1] "dimension of 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    34   9  32   2
  2P GAIN WILD-TYPE 234  60 148   9
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              34               234
  T2               9                60
  T3              32               148
  T4               2                 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"
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    37   3
  2P GAIN WILD-TYPE 197  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     37    3
  2P GAIN WILD-TYPE  197   14
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              37               197
  1               3                14
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    66   8
  2P GAIN WILD-TYPE 352  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     66    8
  2P GAIN WILD-TYPE  352   70
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              66               352
  1               8                70
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    27  50
  2P GAIN WILD-TYPE 162 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     27   50
  2P GAIN WILD-TYPE  162  289
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              27               162
  MALE                50               289
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                11 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-DV-A4W0        TCGA-G6-A8L7 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-MM-A563        TCGA-MM-A84U        TCGA-T7-A92I 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       1                         5    71
  2P GAIN WILD-TYPE     7                        51   386
D3V11, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               5                51
  WHITE                                  71               386
[1] 3 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     4  45
  2P GAIN WILD-TYPE  22 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   45
  2P GAIN WILD-TYPE   22  305
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              45               305
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    55  24
  2Q GAIN WILD-TYPE 296 151
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               79               447 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               24               151 
$`2Q GAIN MUTATED`
TCGA-3Z-A93Z TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3429 TCGA-AK-3444 
       12.66        24.16        18.87         0.10       109.41        48.36 
TCGA-AK-3450 TCGA-B0-4690 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4813 
       49.28         1.41        19.73        57.70        46.59         0.59 
TCGA-B0-5099 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5702 TCGA-B4-5832 TCGA-B4-5838 
       15.95        19.30        38.63        71.41         5.10         5.46 
TCGA-B4-5843 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
        0.36        25.55        23.74         6.38        48.53         0.53 
TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4337 
        4.93       101.06         0.43        77.03        61.78         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4756 
       93.99        18.48        74.17        44.94        31.89        12.30 
TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4799 
       41.75        48.07        13.15        60.59        68.38        37.25 
TCGA-BP-4804 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-5001 TCGA-BP-5173 
       47.97        58.98        31.30         3.88        38.70         1.74 
TCGA-BP-5174 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4644 TCGA-CJ-4876 
       74.20        62.86        37.22        34.95        11.05        64.27 
TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 
       24.66       109.84        47.67        51.25        49.28       131.08 
TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5587 
       72.00       133.71       122.83        53.42       119.64        73.18 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       66.31        74.66        46.16        69.21        58.75         6.77 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5469 TCGA-DV-A4VX 
       79.63        90.54        94.45        10.85        31.10        53.46 
TCGA-EU-5905 
        3.91 

$`2Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       11.90        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.64        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
       22.65         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      117.80        73.08        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        40.01        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         3.32         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        2.53         3.48        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4712 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
        3.25        58.45        15.72         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        52.08        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 
       52.54        30.48        58.59        66.05        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         5.75         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.91        50.14        20.91 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        8.42        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       85.51        94.72        90.28        93.34        32.61        99.85 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       89.36        23.05        62.24        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       21.21        15.16        52.24        62.86        54.77        49.08 
TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       12.23        11.31        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4769 
       77.98        77.62         5.98        44.15        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
       10.82         5.33        61.97        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95        27.22        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 
       43.00        45.07        30.64        41.62        18.51        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        6.35        79.30        30.64        52.27         9.63        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       33.47        19.82        44.55        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61       105.37        58.95        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 
       79.66        10.72        74.27        75.06       116.84        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4894 
       51.52        63.98       115.69        26.93        50.01        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
       39.45        50.24        56.35        49.97       108.56        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       18.81       129.40        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       18.15        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
        5.39        85.78        78.18         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4861 
      103.43        18.77        25.45         0.59        47.08        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
      107.54        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 
       58.82        79.53        23.74        18.44        91.69        55.33 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        1.94        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        81.21        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           133.71            149.16 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            46.16             37.48 
[1] "0.1 - 133.7 (46.2)" "0.1 - 149.2 (37.5)"
[1] "hr=" "1.2"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        35        9        24       11
  2Q GAIN WILD-TYPE     228       48       101       72
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                35               228
  STAGE II                9                48
  STAGE III              24               101
  STAGE IV               11                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"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED    36   9  32   2
  2Q GAIN WILD-TYPE 232  60 148   9
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              36               232
  T2               9                60
  T3              32               148
  T4               2                 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"
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    38   2
  2Q GAIN WILD-TYPE 196  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     38    2
  2Q GAIN WILD-TYPE  196   15
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              38               196
  1               2                15
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    67   9
  2Q GAIN WILD-TYPE 351  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     67    9
  2Q GAIN WILD-TYPE  351   69
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              67               351
  1               9                69
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    31  48
  2Q GAIN WILD-TYPE 158 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     31   48
  2Q GAIN WILD-TYPE  158  291
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              31               158
  MALE                48               291
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                11 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-DV-A4W0        TCGA-G6-A8L7 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-MM-A563        TCGA-MM-A84U        TCGA-T7-A92I 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       1                         5    73
  2Q GAIN WILD-TYPE     7                        51   384
D4V11, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               5                51
  WHITE                                  73               384
[1] 3 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     5  46
  2Q GAIN WILD-TYPE  21 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   46
  2Q GAIN WILD-TYPE   21  304
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              46               304
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    10   9
  3P GAIN WILD-TYPE 341 166
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               507 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                9               166 
$`3P GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-5081 
       43.20        94.19        83.21         3.62        43.96        11.90 
TCGA-B0-5084 TCGA-B4-5835 TCGA-BP-4337 TCGA-BP-4352 TCGA-BP-4969 TCGA-BP-4994 
        7.30         0.53         0.07        11.31        58.98        43.00 
TCGA-BP-5175 TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4897 TCGA-CW-6087 TCGA-CZ-5456 
       30.64        19.82        14.17       109.84         1.35        79.63 
TCGA-CZ-5469 
       31.10 

$`3P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
       15.78        73.68       112.08        68.61       109.51        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       48.36        78.64        40.01        49.28        94.29        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        5.98         2.14        19.73        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.75         5.10         0.85         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
       62.07        80.68        37.25        21.21        15.16        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         6.90        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30         1.74        74.20        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       13.41        24.62        33.47        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 
        0.95       115.00        46.55        63.25        73.22       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66       107.54        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82        79.53        23.74        18.44        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       69.96        84.30        22.52         2.40         1.94        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.07              0.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           109.84            149.16 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            30.64             38.56 
[1] "0.1 - 109.8 (30.6)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.7"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         6        3         4        6
  3P GAIN WILD-TYPE     257       54       121       77
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 6               257
  STAGE II                3                54
  STAGE III               4               121
  STAGE IV                6                77
[1] 4 2
[1] TRUE
[1] "dimension of 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     6   3   9   1
  3P GAIN WILD-TYPE 262  66 171  10
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               6               262
  T2               3                66
  T3               9               171
  T4               1                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"
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     9   3
  3P GAIN WILD-TYPE 225  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9    3
  3P GAIN WILD-TYPE  225   14
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               9               225
  1               3                14
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    13   6
  3P GAIN WILD-TYPE 405  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     13    6
  3P GAIN WILD-TYPE  405   72
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              13               405
  1               6                72
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     9  10
  3P GAIN WILD-TYPE 180 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9   10
  3P GAIN WILD-TYPE  180  329
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               9               180
  MALE                10               329
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         1    18
  3P GAIN WILD-TYPE     8                        55   439
D5V11, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                55
  WHITE                                  18               439
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1  13
  3P GAIN WILD-TYPE  25 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   13
  3P GAIN WILD-TYPE   25  337
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              13               337
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    34  27
  3Q GAIN WILD-TYPE 317 148
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               61               465 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               27               148 
$`3Q GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3374 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 
       38.47        43.20        68.61       109.51        94.19        83.21 
TCGA-B0-4690 TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4833 TCGA-B0-5081 
        1.41         3.62        43.96         6.64        78.44        11.90 
TCGA-B0-5084 TCGA-B0-5097 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5116 TCGA-B0-5696 
        7.30        21.86        90.87        19.30        41.88        85.78 
TCGA-B0-5710 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-4621 
       79.89         0.53         5.46        23.31        25.55        25.91 
TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4337 
        6.38         0.53        93.34        89.36        27.78         0.07 
TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4960 TCGA-BP-4969 
       93.99        11.31         5.98        44.15        71.41        58.98 
TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5198 TCGA-CJ-4638 
       31.30        43.00         6.35        30.64        19.82        14.17 
TCGA-CJ-4640 TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 
      114.41        79.66        66.21       109.84        56.35        47.67 
TCGA-CJ-6028 TCGA-CJ-6033 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4858 
       53.42         7.36        74.66         1.35        18.77        69.21 
TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5469 
        6.77        79.63        94.45        69.96        84.30        31.10 
TCGA-DV-A4VX 
       53.46 

$`3Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       73.68       112.08        46.78        48.36        78.64        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       49.28        94.29        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4834 
       36.53        14.93        54.48        29.10        10.09        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       58.59        66.05        38.63        52.73        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 
      112.80       129.67       133.94        15.78        70.68        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      105.37       130.65       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         5.10         0.85         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       24.23        50.14        16.60        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       94.72        90.28       101.06        32.61        99.85         0.43 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       97.45        53.42         3.58        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       21.21        15.16        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        87.45        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       36.23        28.87        48.10        79.30         1.74        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95       115.00        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       63.25        73.22       106.16        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        83.97        49.25        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06       116.84        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26       118.85        75.58        62.66       119.64 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       66.31        78.18       105.93        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
       46.16         0.59        47.08        58.75        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        21.76        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ 
       11.67        37.15        66.28        56.84        23.90        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           114.41            149.16 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             43.0              38.3 
[1] "0.1 - 114.4 (43.0)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.3"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        17        5        20       19
  3Q GAIN WILD-TYPE     246       52       105       64
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                17               246
  STAGE II                5                52
  STAGE III              20               105
  STAGE IV               19                64
[1] 4 2
[1] TRUE
[1] "dimension of 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    17   6  34   4
  3Q GAIN WILD-TYPE 251  63 146   7
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              17               251
  T2               6                63
  T3              34               146
  T4               4                 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"
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    31   7
  3Q GAIN WILD-TYPE 203  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     31    7
  3Q GAIN WILD-TYPE  203   10
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              31               203
  1               7                10
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    43  17
  3Q GAIN WILD-TYPE 375  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     43   17
  3Q GAIN WILD-TYPE  375   61
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              43               375
  1              17                61
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    20  41
  3Q GAIN WILD-TYPE 169 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     20   41
  3Q GAIN WILD-TYPE  169  298
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              20               169
  MALE                41               298
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                19 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-5158 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E        TCGA-B8-A54F 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4W0        TCGA-G6-A5PC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-MM-A563        TCGA-T7-A92I 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D6V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         4    56
  3Q GAIN WILD-TYPE     8                        52   401
D6V11, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               4                52
  WHITE                                  56               401
[1] 3 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     3  40
  3Q GAIN WILD-TYPE  23 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   40
  3Q GAIN WILD-TYPE   23  310
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                23
  NOT HISPANIC OR LATINO              40               310
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     7   6
  4P GAIN WILD-TYPE 344 169
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               513 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               169 
$`4P GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4688 TCGA-B0-4696 
       43.20        15.78       112.08        94.19         3.32        28.47 
TCGA-B0-4813 TCGA-BP-4166 TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4977 TCGA-BP-4989 
        0.59         0.43        74.17        11.31        14.93         3.88 
TCGA-BP-4994 
       43.00 

$`4P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
       27.22        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.74        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.43              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           112.08            149.16 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            15.78             38.56 
[1] "0.4 - 112.1 (15.8)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.8"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         4        2         5        2
  4P GAIN WILD-TYPE     259       55       120       81
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 4               259
  STAGE II                2                55
  STAGE III               5               120
  STAGE IV                2                81
[1] 4 2
[1] TRUE
[1] "dimension of 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     4   2   6   1
  4P GAIN WILD-TYPE 264  67 174  10
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               4               264
  T2               2                67
  T3               6               174
  T4               1                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"
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     8   1
  4P GAIN WILD-TYPE 226  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8    1
  4P GAIN WILD-TYPE  226   16
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               8               226
  1               1                16
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11   2
  4P GAIN WILD-TYPE 407  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    2
  4P GAIN WILD-TYPE  407   76
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              11               407
  1               2                76
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3  10
  4P GAIN WILD-TYPE 186 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   10
  4P GAIN WILD-TYPE  186  329
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               3               186
  MALE                10               329
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                52 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158        TCGA-CJ-6028 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-DV-A4VX        TCGA-DV-A4VZ        TCGA-DV-A4W0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G6-A8L6        TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V9, continuous
D7V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         1    12
  4P GAIN WILD-TYPE     8                        55   445
D7V11, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                55
  WHITE                                  12               445
[1] 3 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   8
  4P GAIN WILD-TYPE  26 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    8
  4P GAIN WILD-TYPE   26  342
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               8               342
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     8   5
  4Q GAIN WILD-TYPE 343 170
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               513 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               170 
$`4Q GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4696 TCGA-B0-4813 
       43.20        15.78       112.08        94.19        28.47         0.59 
TCGA-BP-4166 TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4977 TCGA-BP-4989 TCGA-BP-4994 
        0.43        74.17        11.31        14.93         3.88        43.00 
TCGA-BP-5177 
        9.63 

$`4Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       58.45        15.72        46.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        31.66        24.82        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         0.85         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       53.65        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       36.95        27.22        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5178 
       79.30         1.74        74.20        30.64        52.27        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.43              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           112.08            149.16 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            15.78             38.56 
[1] "0.4 - 112.1 (15.8)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         5        2         5        1
  4Q GAIN WILD-TYPE     258       55       120       82
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 5               258
  STAGE II                2                55
  STAGE III               5               120
  STAGE IV                1                82
[1] 4 2
[1] TRUE
[1] "dimension of 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     5   2   6   0
  4Q GAIN WILD-TYPE 263  67 174  11
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               5               263
  T2               2                67
  T3               6               174
  T4               0                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"
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   1
  4Q GAIN WILD-TYPE 227  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    1
  4Q GAIN WILD-TYPE  227   16
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               227
  1               1                16
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    12   1
  4Q GAIN WILD-TYPE 406  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     12    1
  4Q GAIN WILD-TYPE  406   77
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              12               406
  1               1                77
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   9
  4Q GAIN WILD-TYPE 185 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    9
  4Q GAIN WILD-TYPE  185  330
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4               185
  MALE                 9               330
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                52 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158        TCGA-CJ-6028 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-DV-A4VX        TCGA-DV-A4VZ        TCGA-DV-A4W0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G6-A8L6        TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V9, continuous
D8V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         1    12
  4Q GAIN WILD-TYPE     8                        55   445
D8V11, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                55
  WHITE                                  12               445
[1] 3 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   7
  4Q GAIN WILD-TYPE  26 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    7
  4Q GAIN WILD-TYPE   26  343
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               7               343
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   135  58
  5P GAIN WILD-TYPE 216 117
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              193               333 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               58               117 
$`5P GAIN MUTATED`
TCGA-3Z-A93Z TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 
       12.66        49.08        48.59        38.99        38.47        48.82 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3374 
       34.29        52.93        88.37        42.97        24.16        43.20 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-A6NL TCGA-A3-A6NN TCGA-AK-3429 TCGA-AK-3430 
       18.87        65.52        22.65         0.10       109.41        15.78 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3460 
      109.51        94.19        78.64        94.29        83.21        82.45 
TCGA-AK-3461 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 
       72.89        28.47         1.38        65.10         5.98        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 
       57.70        43.96         6.64        46.59         5.52        52.21 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4833 
        6.02        40.44        36.53        14.93        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5075 
       40.70        27.42        53.88        29.03         2.27        20.94 
TCGA-B0-5077 TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5102 TCGA-B0-5106 
       43.30        18.51        10.95         8.05        90.87        52.54 
TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5121 TCGA-B0-5694 TCGA-B0-5696 
       19.30        38.63        52.73        48.82        15.78        85.78 
TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5712 TCGA-B0-5713 
       86.47        80.91        71.41       149.16        89.49        91.46 
TCGA-B2-3924 TCGA-B2-4102 TCGA-B2-5635 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-5159 
       35.90        31.30        24.82         5.46        25.55        23.74 
TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54H TCGA-B8-A54I 
       27.02         6.38        48.53         0.53         8.42         4.93 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 
      111.02        94.72       101.06         0.43        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       54.90         0.07        93.99        74.17        62.86        54.77 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 TCGA-BP-4763 
       44.94        31.89        11.31        12.33         5.98        41.75 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4804 
       13.15        68.38        15.78        36.39        37.25        47.97 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4976 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       58.98        48.89        53.65        46.45        31.30        25.81 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4999 
       27.22         3.88        46.45        16.47        43.00        41.62 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5175 
       37.02        37.48        48.10        79.30         1.74        30.64 
TCGA-BP-5177 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5200 TCGA-BP-5201 
        9.63        37.22        13.35        31.79        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4644 TCGA-CJ-4869 
        0.95        46.55        63.25       106.16        11.05        83.97 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4885 TCGA-CJ-4887 
       79.66        74.27       116.84        66.21       113.46        30.64 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4903 
      115.69        50.01       109.84        50.24        56.35        51.25 
TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
      108.56        49.28        54.48       131.08       129.40       133.71 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       22.32       122.83        62.10        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4853 
       53.42        85.78        73.18        66.31        74.66        25.45 
TCGA-CZ-4854 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       46.16        63.39        93.04        61.41        63.42        58.82 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       79.63        90.54        10.85        21.76        69.96        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-DV-5573 
        2.40         1.94        12.69        67.96        12.26        37.15 
TCGA-DV-5574 TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 
       66.28         3.91         4.18        10.29         2.01        19.96 
TCGA-MW-A4EC 
       16.37 

$`5P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       11.90        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3335 
       49.02        37.15        49.58        36.36        37.38        62.01 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3359 
       31.07         4.50        45.53        29.92        18.44        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NI 
       55.76        20.71        18.64        28.31        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
       15.39         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 
      117.80        73.08        73.68       112.08        68.61        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       48.36        40.01        49.28        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       38.40        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4701 
        4.57         2.53         3.48        19.00         3.62         7.82 
TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4816 
        2.14         3.25        58.45        15.72         0.59        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 
       33.50        16.77        54.48        29.10        68.71        45.30 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       26.07        36.85        70.52        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       25.32        15.09         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5116 
       62.89        90.48        30.48        58.59        66.05        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       52.87        51.02        38.43        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 
      111.52       112.80       129.67       133.94        70.68       119.38 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      126.28        73.84       105.37       130.65        79.89       131.15 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
      126.05        32.61         1.68        31.96        21.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.85         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       25.91        50.14        20.91         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       50.14        16.60        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74        17.36        15.42        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 
       85.51        90.28        93.34        32.61        99.85        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       23.05        77.03        62.24        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 
       18.48        52.24        49.08        12.23        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4765 
       12.30        72.59        77.98        77.62        44.15        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        11.64        60.95        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 
       20.38        10.98        36.95         6.71         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       71.41        60.30        14.24        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4993 
       47.11        14.93        36.07        33.34        36.95         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5008 
       45.07        30.64        18.51        38.70        27.62        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5178 
       36.23        28.87         6.35        74.20        52.27        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       74.40        49.15        38.30        42.44        37.25        22.78 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       27.02        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 
       19.82        44.55       115.00        73.22        14.17       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 
       54.61       105.37        58.95        21.24        49.25        10.72 
TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
       75.06        64.27        71.87        61.91        57.83        64.18 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4891 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       51.52        63.98        26.93        24.66        27.65        39.45 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 
       47.67        49.97        49.18        50.33        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5678 
        3.06         4.57        18.81        72.00        25.71        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       25.25        18.15        53.26        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5589 
        7.36        64.57        92.02        81.83         5.39        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4856 
        1.35       105.93        83.90       103.43        18.77         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66       107.54 
TCGA-CZ-4865 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 
        5.46        79.53        23.74        18.44        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5985 
       94.45        10.22        84.30        31.10        80.19        65.65 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.16        11.67        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-G6-A8L8 
       81.21        18.12         6.77         7.96        70.13        35.87 
TCGA-MM-A563 TCGA-MM-A84U TCGA-T7-A92I 
       19.43        23.01        11.70 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           149.16            133.94 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            46.45             36.23 
[1] "0.1 - 149.2 (46.5)" "0.1 - 133.9 (36.2)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED        84       22        55       32
  5P GAIN WILD-TYPE     179       35        70       51
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                84               179
  STAGE II               22                35
  STAGE III              55                70
  STAGE IV               32                51
[1] 4 2
[1] TRUE
[1] "dimension of 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    86  28  75   4
  5P GAIN WILD-TYPE 182  41 105   7
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              86               182
  T2              28                41
  T3              75               105
  T4               4                 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"
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    90   7
  5P GAIN WILD-TYPE 144  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     90    7
  5P GAIN WILD-TYPE  144   10
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              90               144
  1               7                10
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   156  29
  5P GAIN WILD-TYPE 262  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    156   29
  5P GAIN WILD-TYPE  262   49
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             156               262
  1              29                49
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    56 137
  5P GAIN WILD-TYPE 133 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     56  137
  5P GAIN WILD-TYPE  133  202
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              56               133
  MALE               137               202
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       3                        12   176
  5P GAIN WILD-TYPE     5                        44   281
D9V11, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 5
  BLACK OR AFRICAN AMERICAN              12                44
  WHITE                                 176               281
[1] 3 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    10 125
  5P GAIN WILD-TYPE  16 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     10  125
  5P GAIN WILD-TYPE   16  225
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                16
  NOT HISPANIC OR LATINO             125               225
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   144  63
  5Q GAIN WILD-TYPE 207 112
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              207               319 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               63               112 
$`5Q GAIN MUTATED`
TCGA-3Z-A93Z TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 
       12.66        49.08        48.59        38.99        38.47        48.82 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       34.29        52.93        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-A6NL 
       82.32        24.16        43.20        18.87        65.52        22.65 
TCGA-A3-A6NN TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 
        0.10       109.41        15.78       109.51        94.19        48.36 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4693 
       78.64        94.29        83.21        82.45        72.89         2.53 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
       65.10         5.98        19.73        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 
        3.25        46.59         5.52        33.50         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 
       36.53        14.93        10.09        78.44        40.70        27.42 
TCGA-B0-4839 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5088 
       53.88        29.03         2.27        20.94        43.30        18.51 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 
       10.95         8.05        90.87        52.54        58.59        19.30 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5694 TCGA-B0-5696 
       38.63        52.73        38.43        48.82        15.78        85.78 
TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5712 
       86.47        80.91        71.41       149.16        79.89        89.49 
TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4102 TCGA-B2-5635 TCGA-B4-5838 TCGA-B8-4146 
       91.46        35.90        31.30        24.82         5.46        16.80 
TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5550 
       25.55        23.74        27.02        24.23         6.38        48.53 
TCGA-B8-5551 TCGA-B8-A54H TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 
        0.53         8.42         4.93       111.02        94.72       101.06 
TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4338 
        0.43        61.78        64.27        54.90         0.07        93.99 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 
       74.17        62.86        54.77        44.94        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 
       12.33        44.15        41.75        13.15        68.38        15.78 
TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 
       36.39        37.25        47.97        63.62        58.68        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4976 
       61.51         6.74        57.40        58.98        48.89        53.65 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        31.30        25.81        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4999 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5009 
       16.47        43.00        41.62        37.02        37.48        36.23 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5185 
       48.10        79.30         1.74        30.64         9.63        37.22 
TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 
       13.35        31.79        34.95        31.27         0.95        46.55 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 
       63.25       106.16        11.05        83.97        79.66        74.27 
TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4897 
      116.84       113.46        30.64       115.69        50.01       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 
       50.24        56.35        51.25       108.56        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5679 
       54.48         3.06       131.08       129.40       133.71        22.32 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CZ-4853 
       85.78        73.18        66.31        78.18        74.66        25.45 
TCGA-CZ-4854 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       46.16        63.39        93.04        61.41        63.42        58.82 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
       79.63        90.54        91.69        10.85        21.76        69.96 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5986 
       22.52         2.40         1.94        12.69        67.96        12.26 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-A4VX TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A8L6 
       37.15        66.28        53.46         3.91         4.18        10.29 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
        2.01        19.96        16.37 

$`5Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       11.90        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3335 
       49.02        37.15        49.58        36.36        37.38        62.01 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       31.07         4.50        45.53        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.63        74.76        53.29        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A8CQ TCGA-A3-A8OV 
       28.31        20.28        33.47        15.39         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 
       10.62       109.91        29.10       117.80        73.08        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3454 
      112.08        68.61        46.78        40.01        49.28        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       22.45        37.58        38.40        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        3.32         1.41         4.57         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4810 
        1.38         3.62         7.82         2.14        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 
        0.59        52.21        45.07        16.77        54.48        29.10 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       68.71        45.30         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5080 
       65.29        39.45        26.07        36.85        70.52        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5097 
       11.90         7.30        25.32        15.09         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5110 
       52.08        15.95        62.89        90.48        30.48        66.05 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       41.88        52.87        51.02        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 
      111.52       112.80       129.67       133.94        70.68       119.38 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5812 
      126.28        73.84       105.37       130.65       131.15       126.05 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5639 
       32.61         1.68        31.96        21.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4148 
        0.53         4.64         0.36         0.23        23.31        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 
       20.91         1.18         0.85        50.14        16.60        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J 
       14.30        27.29        29.88        17.06         1.74        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4163 
       15.42        16.27        14.17        85.51        90.28        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 
       37.25        21.21        15.16        18.48        52.24        49.08 
TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.23        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       77.62         5.98        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        5.33        61.97        60.59        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4801 
       60.95        48.95        36.53        20.38        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4970 
        6.71         6.94        87.45        71.41        60.30        14.24 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.90        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5000 
       33.34        36.95         5.82        45.07        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 
       38.70        27.62        35.21        28.87         6.35        74.20 
TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       52.27        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.25        22.78        27.02        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4637 
       24.62        33.47        19.82        44.55       115.00        73.22 
TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
       14.17       114.41        54.61       105.37        58.95        21.24 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       49.25        10.72        75.06        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4891 
       61.91        57.83        64.18        51.52        63.98        26.93 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 
       24.66        27.65        39.45        47.67        49.97        49.18 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5677 
       38.56        45.14         4.57        18.81        72.00        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 
       18.87        25.25        18.15        53.26        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4856 
        1.35       105.93        83.90       103.43        18.77         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66       107.54 
TCGA-CZ-4865 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5459 TCGA-CZ-5460 
        5.46        79.53        23.74        18.44        55.33        94.45 
TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5987 
       10.22        84.30        31.10        80.19        65.65        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       11.67        56.84        23.90        12.00        81.21        18.12 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U 
        6.77         7.96        70.13        35.87        19.43        23.01 
TCGA-T7-A92I 
       11.70 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.07              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           149.16            133.94 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            46.16             35.87 
[1] "0.1 - 149.2 (46.2)" "0.1 - 133.9 (35.9)"
[1] "hr=" "1.3"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED        94       23        56       34
  5Q GAIN WILD-TYPE     169       34        69       49
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                94               169
  STAGE II               23                34
  STAGE III              56                69
  STAGE IV               34                49
[1] 4 2
[1] TRUE
[1] "dimension of 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    96  29  79   3
  5Q GAIN WILD-TYPE 172  40 101   8
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              96               172
  T2              29                40
  T3              79               101
  T4               3                 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"
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   100   6
  5Q GAIN WILD-TYPE 134  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    100    6
  5Q GAIN WILD-TYPE  134   11
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0             100               134
  1               6                11
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   167  31
  5Q GAIN WILD-TYPE 251  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    167   31
  5Q GAIN WILD-TYPE  251   47
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0             167               251
  1              31                47
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    61 146
  5Q GAIN WILD-TYPE 128 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     61  146
  5Q GAIN WILD-TYPE  128  193
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              61               128
  MALE               146               193
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       3                        13   189
  5Q GAIN WILD-TYPE     5                        43   268
D10V11, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   3                 5
  BLACK OR AFRICAN AMERICAN              13                43
  WHITE                                 189               268
[1] 3 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    11 137
  5Q GAIN WILD-TYPE  15 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11  137
  5Q GAIN WILD-TYPE   15  213
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                15
  NOT HISPANIC OR LATINO             137               213
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     7   4
  6P GAIN WILD-TYPE 344 171
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11               515 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4               171 
$`6P GAIN MUTATED`
TCGA-A3-3313 TCGA-B0-4811 TCGA-B0-5113 TCGA-B8-5549 TCGA-BP-4781 TCGA-BP-4799 
       24.16        46.59        38.63         6.38        68.38        37.25 
TCGA-BP-4985 TCGA-BP-5177 TCGA-CJ-4885 TCGA-CZ-5457 TCGA-CZ-5460 
       31.30         9.63       113.46        90.54        94.45 

$`6P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       72.89        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 
       30.48        58.59        19.30        66.05        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        5.33        61.97        60.59        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       10.98        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 
        1.74        74.20        30.64        52.27        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 
       18.44        79.63        91.69        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       53.46        12.00        81.21        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             6.38              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           113.46            149.16 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            38.63             38.43 
[1] "6.4 - 113.5 (38.6)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         4        0         5        2
  6P GAIN WILD-TYPE     259       57       120       81
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 4               259
  STAGE II                0                57
  STAGE III               5               120
  STAGE IV                2                81
[1] 4 2
[1] TRUE
[1] "dimension of 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     4   0   7   0
  6P GAIN WILD-TYPE 264  69 173  11
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               4               264
  T2               0                69
  T3               7               173
  T4               0                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"
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6   0
  6P GAIN WILD-TYPE 228  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    0
  6P GAIN WILD-TYPE  228   17
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               6               228
  1               0                17
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     9   2
  6P GAIN WILD-TYPE 409  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9    2
  6P GAIN WILD-TYPE  409   76
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               9               409
  1               2                76
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2   9
  6P GAIN WILD-TYPE 187 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    9
  6P GAIN WILD-TYPE  187  330
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               2               187
  MALE                 9               330
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                52 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-DV-A4VX        TCGA-DV-A4VZ        TCGA-DV-A4W0 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G6-A8L6        TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V9, continuous
D11V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                         1    10
  6P GAIN WILD-TYPE     8                        55   447
D11V11, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                55
  WHITE                                  10               447
[1] 3 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   6
  6P GAIN WILD-TYPE  26 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    6
  6P GAIN WILD-TYPE   26  344
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               6               344
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     5   4
  6Q GAIN WILD-TYPE 346 171
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               517 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               171 
$`6Q GAIN MUTATED`
TCGA-A3-3313 TCGA-B0-4811 TCGA-B0-5113 TCGA-B8-5549 TCGA-BP-4781 TCGA-BP-4799 
       24.16        46.59        38.63         6.38        68.38        37.25 
TCGA-BP-4985 TCGA-CJ-4885 TCGA-CZ-5457 
       31.30       113.46        90.54 

$`6Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       72.89        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 
       30.48        58.59        19.30        66.05        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        5.33        61.97        60.59        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       10.98        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.74        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       61.91        57.83        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        79.63        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       56.84        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             6.38              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           113.46            149.16 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            38.63             38.43 
[1] "6.4 - 113.5 (38.6)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.2"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         3        0         5        1
  6Q GAIN WILD-TYPE     260       57       120       82
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 3               260
  STAGE II                0                57
  STAGE III               5               120
  STAGE IV                1                82
[1] 4 2
[1] TRUE
[1] "dimension of 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     3   0   6   0
  6Q GAIN WILD-TYPE 265  69 174  11
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               3               265
  T2               0                69
  T3               6               174
  T4               0                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"
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     6   0
  6Q GAIN WILD-TYPE 228  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6    0
  6Q GAIN WILD-TYPE  228   17
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               6               228
  1               0                17
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     8   1
  6Q GAIN WILD-TYPE 410  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8    1
  6Q GAIN WILD-TYPE  410   77
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               8               410
  1               1                77
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1   8
  6Q GAIN WILD-TYPE 188 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    8
  6Q GAIN WILD-TYPE  188  331
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               1               188
  MALE                 8               331
[1] 2 2
[1] FALSE
D12V8, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                52 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-DV-A4VX        TCGA-DV-A4VZ        TCGA-DV-A4W0 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G6-A8L6        TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V9, continuous
D12V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         1     8
  6Q GAIN WILD-TYPE     8                        55   449
D12V11, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                55
  WHITE                                   8               449
[1] 3 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   5
  6Q GAIN WILD-TYPE  26 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    5
  6Q GAIN WILD-TYPE   26  345
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               5               345
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   112  59
  7P GAIN WILD-TYPE 239 116
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              171               355 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               59               116 
$`7P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
       24.16        49.08        49.02        48.59        38.99        38.47 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 
       34.29        52.93        42.97        10.49        24.16        43.20 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3425 
       18.87        65.52        20.28         0.10        11.18       109.91 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 
      117.80       109.41        15.78       112.08       109.51        94.19 
TCGA-AK-3444 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       48.36        83.21         3.32         1.41         4.57         3.48 
TCGA-B0-4696 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4811 
       28.47        19.73        57.70        43.96         3.25        46.59 
TCGA-B0-4815 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4852 
       52.21        10.09        27.42        53.88         6.71        36.85 
TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5113 
       43.30        10.95         2.24        90.87        19.30        38.63 
TCGA-B0-5116 TCGA-B0-5694 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5713 
       41.88        15.78       119.38        80.91        73.84        91.46 
TCGA-B2-3924 TCGA-B2-5633 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 
       35.90        31.66         5.10         0.53         5.46         0.36 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5550 TCGA-B8-A54E 
       17.19        25.55        25.91        50.14        48.53        29.88 
TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4167 
        4.93       111.02        85.51       101.06         0.43        89.36 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4332 
       77.03        62.24        61.78        64.27        97.45        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 
       15.16         0.07        93.99        62.86        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4775 
       33.99        77.98        48.07        13.15         5.33        60.59 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       68.38        15.78        36.53        36.39        10.98        37.25 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 
        6.71        47.97        71.41        58.68        60.30         6.74 
TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 
       58.98        48.89        45.50        14.93        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5001 
       36.95         3.88        16.47        43.00        30.64        38.70 
TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5177 TCGA-BP-5178 
       36.23         6.35        79.30         1.74         9.63        62.86 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 
       19.82        34.95        31.27        46.55        63.25        14.17 
TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 
       11.05        79.66        10.72        74.27       116.84       113.46 
TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 
       30.64        63.98       109.84        47.67        51.25        49.28 
TCGA-CJ-4912 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5679 TCGA-CJ-5682 
       54.48         4.57       131.08        72.00        22.32       122.83 
TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6093 
       73.35        53.42        66.31        74.66         1.35       103.43 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5453 
       46.16        47.08        69.21         6.77        61.41        79.53 
TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 
       23.74        79.63        90.54        94.45        10.85        69.96 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5989 TCGA-DV-5565 
       22.52         1.94        31.10        67.96        62.63        13.28 
TCGA-DV-5574 TCGA-G6-A8L7 TCGA-MM-A564 
       66.28        70.13        19.96 

$`7P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       37.15        49.58        36.36        37.38        48.82        62.01 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       31.07         4.50        45.53        29.92        18.44        88.37 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       82.32        51.25        28.70        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-A6NI TCGA-A3-A6NJ 
       55.76        20.71        18.64        28.31        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3431 
       22.65         0.10        10.62        29.10        73.08        73.68 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       68.61        46.78        78.64        40.01        49.28        94.29 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 
       12.13        40.70         1.41         2.53        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 
        3.62        65.10         7.82         5.98         2.14         6.64 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 
       29.10        78.44        68.71        40.70        45.30        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
        2.27        70.52        20.94        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 
       25.32        18.51        15.09         8.05        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       15.95        62.89        90.48        52.54        30.48        58.59 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       66.05        52.73        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 
      133.94        70.68        85.78        86.47       126.28        71.41 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
      126.05        32.61         1.68        31.96        21.30        31.30 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        0.85         4.64         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       42.71        25.05        45.37        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
        0.53        34.39        14.30        27.29        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 
        8.42        17.36        15.42        16.27        14.17        94.72 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4177 
       90.28        93.34        32.61        99.85        23.05        54.90 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4334 
       53.42         3.58        27.78        62.07        80.68        21.21 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        74.17        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 
       12.23        12.33        31.33        12.30        72.59        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 
        5.98        44.15        41.75        71.80        61.68        10.82 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
       61.97        13.51        56.91        11.64        60.95        48.95 
TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 
       20.38        36.95         6.94        87.45        63.62        61.22 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 
       61.51        57.40        14.24        49.38         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4991 
       53.65        36.07        33.34        25.81        27.22        46.45 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 
        5.82        45.07        41.62        18.51        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5174 TCGA-BP-5175 
       37.48        35.21        28.87        48.10        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5202 
       23.47        13.41        24.62        33.47        44.55         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
      115.00        73.22       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 
       58.95        21.24        83.97        49.25        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 
       71.87        66.21        61.91        57.83        64.18        51.52 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       50.24        56.35        49.97       108.56        49.18        50.33 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5676 
       38.56        45.14         3.06        18.81       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 
       25.71        18.87        25.25        18.15        62.10        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       53.26       118.85        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 
       78.18       105.93        83.90        18.77        25.45         0.59 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
       63.42        58.82        18.44        91.69        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       21.76        84.30         2.40        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       12.26        14.63        22.78        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       11.67        37.15        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
       10.29        35.87         2.01        19.43        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           131.08            149.16 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            43.00             37.25 
[1] "0.1 - 131.1 (43.0)" "0.1 - 149.2 (37.2)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED        72       19        45       35
  7P GAIN WILD-TYPE     191       38        80       48
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                72               191
  STAGE II               19                38
  STAGE III              45                80
  STAGE IV               35                48
[1] 4 2
[1] TRUE
[1] "dimension of 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    74  24  69   4
  7P GAIN WILD-TYPE 194  45 111   7
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              74               194
  T2              24                45
  T3              69               111
  T4               4                 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"
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    81   8
  7P GAIN WILD-TYPE 153   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     81    8
  7P GAIN WILD-TYPE  153    9
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              81               153
  1               8                 9
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   130  35
  7P GAIN WILD-TYPE 288  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    130   35
  7P GAIN WILD-TYPE  288   43
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             130               288
  1              35                43
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    46 125
  7P GAIN WILD-TYPE 143 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     46  125
  7P GAIN WILD-TYPE  143  214
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              46               143
  MALE               125               214
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       4                        10   155
  7P GAIN WILD-TYPE     4                        46   302
D13V11, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   4                 4
  BLACK OR AFRICAN AMERICAN              10                46
  WHITE                                 155               302
[1] 3 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     6 104
  7P GAIN WILD-TYPE  20 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6  104
  7P GAIN WILD-TYPE   20  246
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                20
  NOT HISPANIC OR LATINO             104               246
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   110  62
  7Q GAIN WILD-TYPE 241 113
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              172               354 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               62               113 
$`7Q GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
       24.16        49.08        49.02        48.59        38.99        38.47 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 
       34.29        52.93        42.97        10.49        24.16        43.20 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3425 
       18.87        65.52        20.28         0.10        11.18       109.91 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 
      117.80       109.41        15.78       112.08       109.51        94.19 
TCGA-AK-3444 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       48.36        83.21         3.32         1.41         4.57         3.48 
TCGA-B0-4696 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4811 
       28.47        19.73        57.70        43.96         3.25        46.59 
TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       52.21         6.02        10.09        27.42        53.88         6.71 
TCGA-B0-4852 TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5102 TCGA-B0-5109 
       36.85        43.30        10.95         2.24        90.87        19.30 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5694 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5703 
       38.63        41.88        15.78       119.38        80.91        73.84 
TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       91.46        35.90        32.98         5.10         0.53         5.46 
TCGA-B4-5843 TCGA-B8-4146 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
        0.36        16.80        17.19        25.55        25.91        50.14 
TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4162 
       48.53        29.88         4.93       111.02        85.51       101.06 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        0.43        89.36        77.03        62.24        61.78        64.27 
TCGA-BP-4325 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 
       97.45        37.25        15.16         0.07        93.99        62.86 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 
       31.89        11.31        33.99        77.98        48.07        13.15 
TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4798 
        5.33        60.59        68.38        15.78        36.53        10.98 
TCGA-BP-4799 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 
       37.25         6.71        47.97        71.41        58.68        60.30 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4983 
        6.74        58.98        48.89        45.50        14.93        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       31.30        36.95         3.88        16.47        43.00        30.64 
TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5177 TCGA-BP-5178 
       36.23         6.35        79.30         1.74         9.63        62.86 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 
       19.82        34.95        31.27        46.55        63.25        14.17 
TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 
       11.05        79.66        10.72        74.27       116.84       113.46 
TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 
       30.64        63.98       109.84        47.67        51.25        49.28 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5682 
        4.57       131.08        72.00        25.71        22.32       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 
       62.10        73.35        53.42        66.31        74.66         1.35 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
      103.43        18.77        46.16        47.08        69.21         6.77 
TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 
       61.41        23.74        79.63        90.54        94.45        10.85 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5989 
       69.96        22.52         1.94        31.10        67.96        62.63 
TCGA-DV-5565 TCGA-DV-5574 TCGA-G6-A8L7 TCGA-MM-A564 
       13.28        66.28        70.13        19.96 

$`7Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       37.15        49.58        36.36        37.38        48.82        62.01 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       31.07         4.50        45.53        29.92        18.44        88.37 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       82.32        51.25        28.70        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-A6NI TCGA-A3-A6NJ 
       55.76        20.71        18.64        28.31        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3431 
       22.65         0.10        10.62        29.10        73.08        73.68 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       68.61        46.78        78.64        40.01        49.28        94.29 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 
       12.13        40.70         1.41         2.53        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 
        3.62        65.10         7.82         5.98         2.14         6.64 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 
       78.44        68.71        40.70        45.30        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       70.52        20.94        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       18.51        15.09         8.05        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        58.59        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 
       70.68        85.78        86.47       126.28        71.41       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 
      105.37       130.65        79.89       131.15        89.49       126.05 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       32.61         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       24.82        21.57        16.67        12.00         5.75         0.85 
TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        4.64         0.23        23.31        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       45.37        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 
       24.23        50.14        16.60         6.38         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
       14.30        27.29        17.06         1.74         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 
       15.42        16.27        14.17        94.72        90.28        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4327 
       32.61        99.85        23.05        54.90        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07        80.68        21.21        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 
       74.17        54.77        49.08        44.94        12.23        12.33 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       31.33        12.30        72.59        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 
       41.75        71.80        61.68        10.82        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
       56.91        11.64        60.95        48.95        20.38        36.39 
TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 
       36.95         6.94        87.45        63.62        61.22        61.51 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       57.40        14.24        49.38         6.90        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4993 
       36.07        33.34        25.81        27.22        46.45         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       45.07        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5174 TCGA-BP-5175 
       37.48        35.21        28.87        48.10        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5202 
       23.47        13.41        24.62        33.47        44.55         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
      115.00        73.22       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 
       58.95        21.24        83.97        49.25        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 
       71.87        66.21        61.91        57.83        64.18        51.52 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       50.24        56.35        49.97       108.56        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5675 
       54.48        38.56        45.14         3.06        18.81       129.40 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-5689 
      133.71        18.87        25.25        18.15        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
      118.85        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 
      105.93        83.90        25.45         0.59        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
      107.54        63.39        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 
       79.53        18.44        91.69        55.33        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
       84.30         2.40        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       14.63        22.78        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       37.15        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        23.01        16.37        11.70 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           131.08            149.16 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           42.425            37.530 
[1] "0.1 - 131.1 (42.4)" "0.1 - 149.2 (37.5)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED        72       17        45       38
  7Q GAIN WILD-TYPE     191       40        80       45
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                72               191
  STAGE II               17                40
  STAGE III              45                80
  STAGE IV               38                45
[1] 4 2
[1] TRUE
[1] "dimension of 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    74  22  72   4
  7Q GAIN WILD-TYPE 194  47 108   7
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              74               194
  T2              22                47
  T3              72               108
  T4               4                 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"
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    79   8
  7Q GAIN WILD-TYPE 155   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     79    8
  7Q GAIN WILD-TYPE  155    9
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              79               155
  1               8                 9
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   128  38
  7Q GAIN WILD-TYPE 290  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    128   38
  7Q GAIN WILD-TYPE  290   40
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             128               290
  1              38                40
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    48 124
  7Q GAIN WILD-TYPE 141 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     48  124
  7Q GAIN WILD-TYPE  141  215
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              48               141
  MALE               124               215
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       4                        10   156
  7Q GAIN WILD-TYPE     4                        46   301
D14V11, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   4                 4
  BLACK OR AFRICAN AMERICAN              10                46
  WHITE                                 156               301
[1] 3 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     5 107
  7Q GAIN WILD-TYPE  21 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  107
  7Q GAIN WILD-TYPE   21  243
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO             107               243
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    19  12
  8P GAIN WILD-TYPE 332 163
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               31               495 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               163 
$`8P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-AK-3433 TCGA-AK-3445 TCGA-B0-4713 TCGA-B0-4828 
       24.16        49.08       112.08        78.64         6.64        10.09 
TCGA-B0-4844 TCGA-B0-5097 TCGA-B0-5109 TCGA-B4-5832 TCGA-BP-4342 TCGA-BP-4768 
       10.29        21.86        19.30         5.10        74.17        13.15 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-5000 TCGA-BP-5185 TCGA-BP-5191 TCGA-CJ-4871 
       46.45        31.30        18.51        37.22        31.79        79.66 
TCGA-CJ-4901 TCGA-CJ-4923 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4866 
       47.67        18.81        66.31        74.66        69.21        61.41 
TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 TCGA-DV-A4VX 
       79.63        69.96        31.10        12.69        14.63        53.46 
TCGA-MM-A564 
       19.96 

$`8P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.47        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       73.68        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 
        5.98         2.14        19.73        57.70        43.96         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       14.93        54.48        29.10        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        58.59        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67        12.00         5.75         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       33.34        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.74        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95       115.00        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      105.37        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       27.65        39.45       109.84        50.24        56.35        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 
       38.56        45.14         3.06         4.57       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45        46.16         0.59        47.08        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66       107.54        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
       22.52         2.40         1.94        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       12.26        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.00        81.21        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             5.10              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           112.08            149.16 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            31.79             38.56 
[1] "5.1 - 112.1 (31.8)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         6        8         9        8
  8P GAIN WILD-TYPE     257       49       116       75
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 6               257
  STAGE II                8                49
  STAGE III               9               116
  STAGE IV                8                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED     6   9  16   0
  8P GAIN WILD-TYPE 262  60 164  11
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               6               262
  T2               9                60
  T3              16               164
  T4               0                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"
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    13   1
  8P GAIN WILD-TYPE 221  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     13    1
  8P GAIN WILD-TYPE  221   16
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              13               221
  1               1                16
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    22   7
  8P GAIN WILD-TYPE 396  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     22    7
  8P GAIN WILD-TYPE  396   71
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              22               396
  1               7                71
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     9  22
  8P GAIN WILD-TYPE 180 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   22
  8P GAIN WILD-TYPE  180  317
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               9               180
  MALE                22               317
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                19 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3451 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621        TCGA-B8-5158 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E        TCGA-B8-A54F 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4W0        TCGA-G6-A5PC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-MM-A563        TCGA-T7-A92I 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V10, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                11 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3451        TCGA-B2-A4SR 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5550        TCGA-DV-A4W0        TCGA-G6-A8L7 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-MM-A563        TCGA-MM-A84U        TCGA-T7-A92I 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       1                         3    26
  8P GAIN WILD-TYPE     7                        53   431
D15V11, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                53
  WHITE                                  26               431
[1] 3 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     0  20
  8P GAIN WILD-TYPE  26 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   20
  8P GAIN WILD-TYPE   26  330
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              20               330
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    38  24
  8Q GAIN WILD-TYPE 313 151
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               62               464 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               24               151 
$`8Q GAIN MUTATED`
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 
        0.53        24.16        49.08        37.15        38.47        34.29 
TCGA-AK-3425 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3445 TCGA-B0-4688 TCGA-B0-4712 
      109.91       112.08        68.61        78.64         3.32        43.96 
TCGA-B0-4713 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5081 TCGA-B0-5097 TCGA-B0-5108 
        6.64        10.09        10.29        11.90        21.86        58.59 
TCGA-B0-5109 TCGA-B4-5832 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I 
       19.30         5.10        20.91        27.02         0.53         4.93 
TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4798 
       61.78        93.99        74.17         5.98        13.15        10.98 
TCGA-BP-4799 TCGA-BP-4962 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-5000 TCGA-BP-5169 
       37.25        58.68        46.45        31.30        18.51         6.35 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5185 TCGA-BP-5191 TCGA-CJ-4871 TCGA-CJ-4881 
        1.74        30.64        37.22        31.79        79.66        66.21 
TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-4923 TCGA-CJ-5677 TCGA-CJ-6033 TCGA-CW-5588 
       47.67        54.48        18.81        25.71         7.36        66.31 
TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5462 
       74.66        46.16        69.21        61.41        79.63        10.22 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 
       69.96        22.52         1.94        31.10        12.69        14.63 
TCGA-DV-A4VX TCGA-MM-A564 
       53.46        19.96 

$`8Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3317 
       12.66        11.90        36.82        47.21        39.16        49.02 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       49.58        48.59        36.36        38.99        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       62.01        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68       109.51        94.19        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        1.41         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        19.73        57.70         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5110 TCGA-B0-5113 
       90.87        90.48        52.54        30.48        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.75         0.85         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 
       45.37        17.19        25.55        25.91        50.14        23.74 
TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
        1.18         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
       48.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        1.74         8.42        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
        0.07        18.48        52.24        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       44.94        12.23        31.89        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       31.33        12.30        72.59        77.98        77.62        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       63.62        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 
       47.11        53.65        14.93        36.07        33.34        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
       43.00        45.07        30.64        41.62        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       79.30        74.20        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       27.02        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61       105.37        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       49.25        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       27.65        39.45       109.84        50.24        56.35        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 
       51.25       108.56        49.18        49.28        50.33        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
       45.14         3.06         4.57       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
      133.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66       119.64        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
        5.39        85.78        73.18        78.18         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        18.77        25.45         0.59        47.08 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
       90.54        91.69        55.33        94.45        10.85        21.76 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       84.30         2.40        80.19        67.96        65.65        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ 
       11.67        37.15        66.28        56.84        23.90        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U 
       10.29        70.13        35.87         2.01        19.43        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.53              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           112.08            149.16 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            31.20             39.45 
[1] "0.5 - 112.1 (31.2)" "0.1 - 149.2 (39.5)"
[1] "hr=" "1.4"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED        18       11        19       14
  8Q GAIN WILD-TYPE     245       46       106       69
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                18               245
  STAGE II               11                46
  STAGE III              19               106
  STAGE IV               14                69
[1] 4 2
[1] TRUE
[1] "dimension of 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    19  12  30   1
  8Q GAIN WILD-TYPE 249  57 150  10
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              19               249
  T2              12                57
  T3              30               150
  T4               1                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"
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    27   3
  8Q GAIN WILD-TYPE 207  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     27    3
  8Q GAIN WILD-TYPE  207   14
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              27               207
  1               3                14
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    45  14
  8Q GAIN WILD-TYPE 373  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     45   14
  8Q GAIN WILD-TYPE  373   64
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              45               373
  1              14                64
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    16  46
  8Q GAIN WILD-TYPE 173 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     16   46
  8Q GAIN WILD-TYPE  173  293
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              16               173
  MALE                46               293
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                10 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3451        TCGA-B2-A4SR 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B8-5550        TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-MM-A563 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-MM-A84U        TCGA-T7-A92I 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       1                         5    54
  8Q GAIN WILD-TYPE     7                        51   403
D16V11, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               5                51
  WHITE                                  54               403
[1] 3 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  37
  8Q GAIN WILD-TYPE  25 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   37
  8Q GAIN WILD-TYPE   25  313
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              37               313
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    10   3
  9P GAIN WILD-TYPE 341 172
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               513 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               172 
$`9P GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4698 TCGA-BP-4331 
       43.20       109.41       112.08        94.19         1.38        80.68 
TCGA-BP-4770 TCGA-BP-4969 TCGA-BP-5181 TCGA-CJ-4870 TCGA-CJ-4897 TCGA-CZ-4866 
       10.82        58.98        49.15        49.25       109.84        61.41 
TCGA-CZ-5457 
       90.54 

$`9P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
       10.62       109.91        29.10       117.80        73.08        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        31.66        24.82        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       53.42         3.58        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       83.97        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66       107.54        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.38              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           112.08            149.16 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            61.41             37.48 
[1] "1.4 - 112.1 (61.4)" "0.1 - 149.2 (37.5)"
[1] "hr=" "2.2"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         6        2         3        2
  9P GAIN WILD-TYPE     257       55       122       81
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 6               257
  STAGE II                2                55
  STAGE III               3               122
  STAGE IV                2                81
[1] 4 2
[1] TRUE
[1] "dimension of 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     6   2   3   2
  9P GAIN WILD-TYPE 262  67 177   9
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               6               262
  T2               2                67
  T3               3               177
  T4               2                 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"
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     5   0
  9P GAIN WILD-TYPE 229  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    0
  9P GAIN WILD-TYPE  229   17
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               5               229
  1               0                17
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    13   0
  9P GAIN WILD-TYPE 405  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     13    0
  9P GAIN WILD-TYPE  405   78
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              13               405
  1               0                78
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     9   4
  9P GAIN WILD-TYPE 180 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      9    4
  9P GAIN WILD-TYPE  180  335
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               9               180
  MALE                 4               335
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                52 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-DV-A4VX        TCGA-DV-A4VZ        TCGA-DV-A4W0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G6-A8L6        TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D17V9, continuous
D17V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         2    11
  9P GAIN WILD-TYPE     8                        54   446
D17V11, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               2                54
  WHITE                                  11               446
[1] 3 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     1  10
  9P GAIN WILD-TYPE  25 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   10
  9P GAIN WILD-TYPE   25  340
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              10               340
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     8   4
  9Q GAIN WILD-TYPE 343 171
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               514 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               171 
$`9Q GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4688 TCGA-B0-4698 
       43.20       109.41       112.08        94.19         3.32         1.38 
TCGA-BP-4770 TCGA-BP-4969 TCGA-CJ-4897 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5468 
       10.82        58.98       109.84        61.41        90.54         1.94 

$`9Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
       10.62       109.91        29.10       117.80        73.08        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        1.41         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
       19.00         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        31.66        24.82        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         0.85         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       79.63        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 
       21.76        69.96        84.30        22.52         2.40        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.00        81.21        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.38              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           112.08            149.16 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           60.195            38.350 
[1] "1.4 - 112.1 (60.2)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         4        2         2        4
  9Q GAIN WILD-TYPE     259       55       123       79
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 4               259
  STAGE II                2                55
  STAGE III               2               123
  STAGE IV                4                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED     4   2   3   3
  9Q GAIN WILD-TYPE 264  67 177   8
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               4               264
  T2               2                67
  T3               3               177
  T4               3                 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"
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     5   0
  9Q GAIN WILD-TYPE 229  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    0
  9Q GAIN WILD-TYPE  229   17
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               5               229
  1               0                17
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    10   2
  9Q GAIN WILD-TYPE 408  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     10    2
  9Q GAIN WILD-TYPE  408   76
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              10               408
  1               2                76
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     7   5
  9Q GAIN WILD-TYPE 182 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      7    5
  9Q GAIN WILD-TYPE  182  334
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               7               182
  MALE                 5               334
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                52 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-DV-A4VX        TCGA-DV-A4VZ        TCGA-DV-A4W0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G6-A8L6        TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D18V9, continuous
D18V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         1    11
  9Q GAIN WILD-TYPE     8                        55   446
D18V11, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                55
  WHITE                                  11               446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  10
  9Q GAIN WILD-TYPE  25 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   10
  9Q GAIN WILD-TYPE   25  340
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              10               340
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    11   6
  10P GAIN WILD-TYPE 340 169
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                509 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                169 
$`10P GAIN MUTATED`
TCGA-A3-3316 TCGA-AK-3453 TCGA-B0-4690 TCGA-B0-5109 TCGA-B4-5832 TCGA-B4-5838 
       49.08        83.21         1.41        19.30         5.10         5.46 
TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-5175 TCGA-CW-5588 
       93.99        74.17        13.15        68.38        30.64        66.31 
TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5468 TCGA-EU-5905 
       69.21        61.41        23.74         1.94         3.91 

$`10P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         3.32         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       40.44        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       58.59        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
      111.52       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         5.75         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
       15.16         0.07        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       48.10         6.35        79.30         1.74        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95       115.00        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      105.37        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        58.75         6.77        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82        79.53 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       23.90        53.46        12.00        81.21        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.41               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             93.99             149.16 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             30.64              38.47 
[1] "1.4 - 94.0 (30.6)"  "0.1 - 149.2 (38.5)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         7        4         2        4
  10P GAIN WILD-TYPE     256       53       123       79
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  7                256
  STAGE II                 4                 53
  STAGE III                2                123
  STAGE IV                 4                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED     7   5   4   1
  10P GAIN WILD-TYPE 261  64 176  10
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                7                261
  T2                5                 64
  T3                4                176
  T4                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     6   2
  10P GAIN WILD-TYPE 228  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    2
  10P GAIN WILD-TYPE  228   15
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                6                228
  1                2                 15
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    14   3
  10P GAIN WILD-TYPE 404  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     14    3
  10P GAIN WILD-TYPE  404   75
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               14                404
  1                3                 75
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     5  12
  10P GAIN WILD-TYPE 184 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5   12
  10P GAIN WILD-TYPE  184  327
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                5                184
  MALE                 12                327
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0    17
  10P GAIN WILD-TYPE     8                        56   440
D19V11, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 56
  WHITE                                   17                440
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  10
  10P GAIN WILD-TYPE  26 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   10
  10P GAIN WILD-TYPE   26  340
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               10                340
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     8   4
  10Q GAIN WILD-TYPE 343 171
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                514 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                171 
$`10Q GAIN MUTATED`
TCGA-AK-3453 TCGA-B0-5109 TCGA-B4-5832 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4781 
       83.21        19.30         5.10        11.31        13.15        68.38 
TCGA-BP-5175 TCGA-CW-5588 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5468 TCGA-EU-5905 
       30.64        66.31        69.21        61.41         1.94         3.91 

$`10Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       94.19        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       94.29        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       72.89        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        58.59        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       80.68        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
       61.97        60.59        13.51        56.91        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30         1.74        74.20        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        81.21        18.12         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.94               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             83.21             149.16 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            24.970             38.515 
[1] "1.9 - 83.2 (25.0)"  "0.1 - 149.2 (38.5)"
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         6        2         2        2
  10Q GAIN WILD-TYPE     257       55       123       81
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  6                257
  STAGE II                 2                 55
  STAGE III                2                123
  STAGE IV                 2                 81
[1] 4 2
[1] TRUE
[1] "dimension of 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     6   2   4   0
  10Q GAIN WILD-TYPE 262  67 176  11
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                6                262
  T2                2                 67
  T3                4                176
  T4                0                 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"
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   1
  10Q GAIN WILD-TYPE 231  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    1
  10Q GAIN WILD-TYPE  231   16
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                3                231
  1                1                 16
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    10   2
  10Q GAIN WILD-TYPE 408  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     10    2
  10Q GAIN WILD-TYPE  408   76
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               10                408
  1                2                 76
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     6   6
  10Q GAIN WILD-TYPE 183 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    6
  10Q GAIN WILD-TYPE  183  333
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                6                183
  MALE                  6                333
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0    12
  10Q GAIN WILD-TYPE     8                        56   445
D20V11, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 56
  WHITE                                   12                445
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   8
  10Q GAIN WILD-TYPE  26 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    8
  10Q GAIN WILD-TYPE   26  342
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                8                342
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    22   9
  11P GAIN WILD-TYPE 329 166
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                495 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                166 
$`11P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3372 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4710 
       24.16        24.16       112.08        94.19        83.21        57.70 
TCGA-B0-4844 TCGA-B0-5113 TCGA-B4-5832 TCGA-B8-4620 TCGA-B8-A54I TCGA-BP-4167 
       10.29        38.63         5.10        25.55         4.93        89.36 
TCGA-BP-4337 TCGA-BP-4351 TCGA-BP-4799 TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5200 
        0.07        31.89        37.25        43.00        37.22        34.95 
TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4885 TCGA-CJ-4907 TCGA-CJ-5679 
       46.55        11.05        79.66       113.46        49.28        22.32 
TCGA-CJ-5682 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5468 
      122.83        69.21         6.77        61.41        94.45         1.94 
TCGA-EU-5905 
        3.91 

$`11P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       40.01        49.28        94.29        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        2.14        19.73        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       52.54        30.48        58.59        19.30        66.05        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       17.19        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
       17.06         1.74         8.42        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
       93.34        32.61        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       15.16        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.74        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        31.27         0.95       115.00        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        49.25        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.25       108.56        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       18.87        25.25        18.15        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       47.08        58.75        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 
       79.63        90.54        91.69        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 
       21.76        69.96        84.30        22.52         2.40        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        81.21        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            122.83             149.16 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             37.25              38.47 
[1] "0.1 - 122.8 (37.2)" "0.1 - 149.2 (38.5)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         8        4        11        8
  11P GAIN WILD-TYPE     255       53       114       75
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  8                255
  STAGE II                 4                 53
  STAGE III               11                114
  STAGE IV                 8                 75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED     8   4  18   1
  11P GAIN WILD-TYPE 260  65 162  10
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                8                260
  T2                4                 65
  T3               18                162
  T4                1                 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"
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    10   0
  11P GAIN WILD-TYPE 224  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10    0
  11P GAIN WILD-TYPE  224   17
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               10                224
  1                0                 17
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    22   8
  11P GAIN WILD-TYPE 396  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     22    8
  11P GAIN WILD-TYPE  396   70
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               22                396
  1                8                 70
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    10  21
  11P GAIN WILD-TYPE 179 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10   21
  11P GAIN WILD-TYPE  179  318
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               10                179
  MALE                 21                318
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         2    29
  11P GAIN WILD-TYPE     8                        54   428
D21V11, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 54
  WHITE                                   29                428
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  19
  11P GAIN WILD-TYPE  25 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   19
  11P GAIN WILD-TYPE   25  331
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               19                331
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    22   7
  11Q GAIN WILD-TYPE 329 168
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                497 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                168 
$`11Q GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3372 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4710 
       24.16        24.16       112.08        94.19        83.21        57.70 
TCGA-B0-4844 TCGA-B0-5113 TCGA-B2-4099 TCGA-B8-4620 TCGA-B8-A54I TCGA-BP-4167 
       10.29        38.63        31.96        25.55         4.93        89.36 
TCGA-BP-4337 TCGA-BP-4351 TCGA-BP-4799 TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5200 
        0.07        31.89        37.25        43.00        37.22        34.95 
TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4885 TCGA-CJ-4907 TCGA-CJ-5679 
       46.55        11.05        79.66       113.46        49.28        22.32 
TCGA-CJ-5682 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-EU-5905 
      122.83        69.21        61.41        94.45         3.91 

$`11Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       40.01        49.28        94.29        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        2.14        19.73        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       52.54        30.48        58.59        19.30        66.05        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       17.19        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
       17.06         1.74         8.42        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
       93.34        32.61        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       15.16        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.74        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        31.27         0.95       115.00        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        49.25        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.25       108.56        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       18.87        25.25        18.15        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 
       18.44        79.63        90.54        91.69        55.33        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       23.90        53.46        12.00        81.21        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            122.83             149.16 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             38.63              38.43 
[1] "0.1 - 122.8 (38.6)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.6"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         9        4        10        6
  11Q GAIN WILD-TYPE     254       53       115       77
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  9                254
  STAGE II                 4                 53
  STAGE III               10                115
  STAGE IV                 6                 77
[1] 4 2
[1] TRUE
[1] "dimension of 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     9   4  16   0
  11Q GAIN WILD-TYPE 259  65 164  11
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                9                259
  T2                4                 65
  T3               16                164
  T4                0                 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"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     9   0
  11Q GAIN WILD-TYPE 225  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      9    0
  11Q GAIN WILD-TYPE  225   17
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                9                225
  1                0                 17
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    22   6
  11Q GAIN WILD-TYPE 396  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     22    6
  11Q GAIN WILD-TYPE  396   72
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               22                396
  1                6                 72
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    10  19
  11Q GAIN WILD-TYPE 179 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10   19
  11Q GAIN WILD-TYPE  179  320
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               10                179
  MALE                 19                320
[1] 2 2
[1] FALSE
D22V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4860 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5465 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4VX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-A4VZ         TCGA-DV-A4W0         TCGA-EU-5904 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EU-5906         TCGA-EU-5907         TCGA-G6-A8L6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-G6-A8L8         TCGA-T7-A92I 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V9, continuous
D22V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         2    27
  11Q GAIN WILD-TYPE     8                        54   430
D22V11, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 54
  WHITE                                   27                430
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  18
  11Q GAIN WILD-TYPE  25 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   18
  11Q GAIN WILD-TYPE   25  332
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               18                332
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    70  51
  12P GAIN WILD-TYPE 281 124
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               121                405 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                51                124 
$`12P GAIN MUTATED`
TCGA-A3-3311 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3372 
       39.16        37.15        38.47        52.93        42.97        24.16 
TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3387 TCGA-A3-A6NI TCGA-AK-3425 TCGA-AK-3430 
       43.20        18.87        20.28        33.47       109.91        15.78 
TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 
      112.08       109.51        94.19        83.21         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4710 
        4.57         2.53         1.38         3.62        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 
       43.96         6.64        46.59        52.21         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4848 TCGA-B0-5075 
       36.53        14.93        10.09        27.42        29.03        20.94 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5107 TCGA-B0-5109 
       11.90         7.30        10.95         8.05        30.48        19.30 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5713 TCGA-B4-5832 
       38.63        41.88        85.78        86.47        91.46         5.10 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5163 TCGA-B8-5551 
        5.46        23.31        25.91        50.14        27.02         0.53 
TCGA-B8-A54F TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4174 
       17.06         4.93       101.06        93.34        89.36        61.78 
TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4761 
       64.27         0.07        93.99        31.89        11.31         5.98 
TCGA-BP-4768 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       13.15        11.64        15.78         6.71        47.97        71.41 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4988 
       60.30        61.22        14.93        46.45        31.30        27.22 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5009 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5178 
       16.47        43.00        36.23         1.74        30.64        62.86 
TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5194 TCGA-BP-5200 TCGA-CJ-4636 TCGA-CJ-4638 
       37.22        31.79        13.41        34.95        63.25        14.17 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4884 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 
       10.72        74.27        57.83        51.25        49.28        54.48 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 
        4.57        18.81       131.08       133.71        22.32       122.83 
TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CZ-4854 
       73.35        53.42        66.31        74.66         1.35        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5464 
        0.59        47.08        61.41        79.63        10.85        69.96 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5987 TCGA-DV-A4VX 
       22.52         1.94        31.10        67.96        14.63        53.46 
TCGA-EU-5905 
        3.91 

$`12P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 
       12.66        11.90        36.82        47.21         0.53        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.08        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        62.01        34.29        31.07         4.50 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        18.44        88.37        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 
       10.49        28.70        74.63        74.76        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL 
       20.71        18.64        28.31        65.52        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 
        0.10         0.10        11.18        10.62        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 
       73.08       109.41        73.68        68.61        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       78.64        40.01        49.28        94.29        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 
        1.41         3.48        28.47        19.00        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
        5.98         2.14         3.25        58.45        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 
        5.52        45.07        33.50        16.77        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 
       78.44        68.71        40.70        45.30        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 
        2.27        36.85        70.52        43.30        11.24        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       18.51        15.09         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.87        90.48        52.54        58.59        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       15.78        70.68       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        31.66        24.82        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         5.75         0.85         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       45.37        17.19        25.55        20.91        23.74         1.18 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G TCGA-B8-A54H 
       34.39        14.30        27.29        29.88         1.74         8.42 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       94.72        90.28        32.61        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       77.03        62.24        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98        77.62        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        68.38        60.95        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4807 
       20.38        36.39        10.98        37.25        36.95         6.94 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       87.45        63.62        58.68        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 
       47.11        53.65        36.07        33.34        25.81        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        3.88        46.45         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 
       28.87        48.10         6.35        79.30        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5195 
       22.78        13.35        27.02        33.24        23.47        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       33.47        19.82        44.55        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       46.55        73.22       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97       108.56        49.18 
TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5672 TCGA-CJ-5675 
       50.33        38.56        45.14         3.06        72.00       129.40 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 
       25.71        18.87        25.25        18.15        62.10        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       53.26       118.85        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       78.18       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 
       18.44        90.54        91.69        55.33        94.45        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       21.76        84.30         2.40        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       12.26        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        81.21        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            133.71             149.16 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             31.89              40.70 
[1] "0.1 - 133.7 (31.9)" "0.1 - 149.2 (40.7)"
[1] "hr=" "1.6"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED        44        9        38       30
  12P GAIN WILD-TYPE     219       48        87       53
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                 44                219
  STAGE II                 9                 48
  STAGE III               38                 87
  STAGE IV                30                 53
[1] 4 2
[1] TRUE
[1] "dimension of 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    46  13  58   4
  12P GAIN WILD-TYPE 222  56 122   7
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               46                222
  T2               13                 56
  T3               58                122
  T4                4                  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"
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    57   8
  12P GAIN WILD-TYPE 177   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     57    8
  12P GAIN WILD-TYPE  177    9
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               57                177
  1                8                  9
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    90  27
  12P GAIN WILD-TYPE 328  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     90   27
  12P GAIN WILD-TYPE  328   51
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               90                328
  1               27                 51
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    39  82
  12P GAIN WILD-TYPE 150 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     39   82
  12P GAIN WILD-TYPE  150  257
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               39                150
  MALE                 82                257
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       2                         7   110
  12P GAIN WILD-TYPE     6                        49   347
D23V11, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                7                 49
  WHITE                                  110                347
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3  82
  12P GAIN WILD-TYPE  23 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   82
  12P GAIN WILD-TYPE   23  268
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               82                268
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    71  51
  12Q GAIN WILD-TYPE 280 124
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               122                404 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                51                124 
$`12Q GAIN MUTATED`
TCGA-A3-3311 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3372 
       39.16        37.15        38.47        52.93        42.97        24.16 
TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3387 TCGA-A3-A6NI TCGA-AK-3425 TCGA-AK-3430 
       43.20        18.87        20.28        33.47       109.91        15.78 
TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 
      112.08       109.51        94.19        83.21         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 
        4.57         2.53        28.47         1.38         3.62        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4819 
       57.70        43.96         6.64        46.59        52.21         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4848 
       40.44        36.53        14.93        10.09        27.42        29.03 
TCGA-B0-5075 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5107 TCGA-B0-5109 
       20.94        11.90         7.30        10.95        30.48        19.30 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5713 TCGA-B4-5832 
       38.63        41.88        85.78        86.47        91.46         5.10 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5163 TCGA-B8-5551 
        5.46        23.31        25.91        50.14        27.02         0.53 
TCGA-B8-A54F TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4174 
       17.06         4.93       101.06        93.34        89.36        61.78 
TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4761 
       64.27         0.07        93.99        31.89        11.31         5.98 
TCGA-BP-4768 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       13.15        11.64        15.78         6.71        47.97        71.41 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4988 
       60.30        61.22        14.93        46.45        31.30        27.22 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5009 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5178 
       16.47        43.00        36.23         1.74        30.64        62.86 
TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5194 TCGA-BP-5200 TCGA-CJ-4636 TCGA-CJ-4638 
       37.22        31.79        13.41        34.95        63.25        14.17 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4903 TCGA-CJ-4907 
       10.72        74.27        66.21        57.83        51.25        49.28 
TCGA-CJ-4912 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 
       54.48         4.57        18.81       131.08       133.71        22.32 
TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 
      122.83        73.35        53.42        66.31        74.66         1.35 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5461 
       46.16         0.59        47.08        61.41        79.63        10.85 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5987 
       69.96        22.52         1.94        31.10        67.96        14.63 
TCGA-DV-A4VX TCGA-EU-5905 
       53.46         3.91 

$`12Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 
       12.66        11.90        36.82        47.21         0.53        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.08        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        62.01        34.29        31.07         4.50 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        18.44        88.37        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 
       10.49        28.70        74.63        74.76        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL 
       20.71        18.64        28.31        65.52        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 
        0.10         0.10        11.18        10.62        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 
       73.08       109.41        73.68        68.61        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       78.64        40.01        49.28        94.29        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        1.41         3.48        19.00        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 
        2.14         3.25        58.45        15.72         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       45.07        33.50        16.77        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       68.71        40.70        45.30        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 
       10.52        10.29        65.29        39.45        26.07         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 
       36.85        70.52        43.30        11.24        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       15.09         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.87        90.48        52.54        58.59        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       15.78        70.68       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        31.66        24.82        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         5.75         0.85         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       45.37        17.19        25.55        20.91        23.74         1.18 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G TCGA-B8-A54H 
       34.39        14.30        27.29        29.88         1.74         8.42 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       94.72        90.28        32.61        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       77.03        62.24        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98        77.62        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        68.38        60.95        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4807 
       20.38        36.39        10.98        37.25        36.95         6.94 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       87.45        63.62        58.68        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 
       47.11        53.65        36.07        33.34        25.81        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        3.88        46.45         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 
       28.87        48.10         6.35        79.30        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5195 
       22.78        13.35        27.02        33.24        23.47        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       33.47        19.82        44.55        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       46.55        73.22       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4885 
       75.06       116.84        64.27        71.87        61.91       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       56.35        47.67        49.97       108.56        49.18        50.33 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
       38.56        45.14         3.06        72.00       129.40        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-5689 
       18.87        25.25        18.15        62.10        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
      118.85        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4858 
      105.93        83.90       103.43        18.77        25.45        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 
       90.54        91.69        55.33        94.45        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
       84.30         2.40        12.69        80.19        65.65        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ 
       11.67        37.15        66.28        56.84        23.90        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       81.21        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            133.71             149.16 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            32.680             40.355 
[1] "0.1 - 133.7 (32.7)" "0.1 - 149.2 (40.4)"
[1] "hr=" "1.5"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED        44        9        39       30
  12Q GAIN WILD-TYPE     219       48        86       53
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                 44                219
  STAGE II                 9                 48
  STAGE III               39                 86
  STAGE IV                30                 53
[1] 4 2
[1] TRUE
[1] "dimension of 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    46  13  59   4
  12Q GAIN WILD-TYPE 222  56 121   7
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               46                222
  T2               13                 56
  T3               59                121
  T4                4                  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"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    57   8
  12Q GAIN WILD-TYPE 177   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     57    8
  12Q GAIN WILD-TYPE  177    9
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               57                177
  1                8                  9
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    91  27
  12Q GAIN WILD-TYPE 327  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     91   27
  12Q GAIN WILD-TYPE  327   51
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               91                327
  1               27                 51
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    39  83
  12Q GAIN WILD-TYPE 150 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     39   83
  12Q GAIN WILD-TYPE  150  256
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               39                150
  MALE                 83                256
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         7   111
  12Q GAIN WILD-TYPE     6                        49   346
D24V11, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                7                 49
  WHITE                                  111                346
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3  83
  12Q GAIN WILD-TYPE  23 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   83
  12Q GAIN WILD-TYPE   23  267
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               83                267
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    17   5
  13Q GAIN WILD-TYPE 334 170
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                504 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                170 
$`13Q GAIN MUTATED`
TCGA-A3-3325 TCGA-AK-3453 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5690 TCGA-B2-5639 
       38.47        83.21         2.14        57.70       111.52        32.98 
TCGA-BP-4166 TCGA-BP-4332 TCGA-BP-4983 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4905 
        0.43        37.25        46.45        19.82        34.95        49.18 
TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5689 
       49.28        54.48       131.08       133.71       122.83        53.26 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-DV-5574 
       94.45        10.85        69.96        66.28 

$`13Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       12.13        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        2.53         3.48        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 
       65.10         7.82         5.98        19.73        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        24.82        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         0.85         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       27.78        62.07        80.68        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 
       47.11        53.65        14.93        36.07        33.34        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.74        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        44.55        31.27         0.95       115.00        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      105.37        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-4913 
       47.67        49.97        51.25       108.56        50.33        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 
       45.14         3.06         4.57        18.81        72.00       129.40 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
       25.71        18.87        22.32        25.25        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
      107.54        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       91.69        55.33        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5575 
       45.96        65.88        12.16        11.67        37.15        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.43               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            133.71             149.16 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             51.27              37.53 
[1] "0.4 - 133.7 (51.3)" "0.1 - 149.2 (37.5)"
[1] "hr=" "2"  
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         6        3         8        5
  13Q GAIN WILD-TYPE     257       54       117       78
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  6                257
  STAGE II                 3                 54
  STAGE III                8                117
  STAGE IV                 5                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED     7   3  12   0
  13Q GAIN WILD-TYPE 261  66 168  11
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                261
  T2                3                 66
  T3               12                168
  T4                0                 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"
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 230  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  230   17
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                4                230
  1                0                 17
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    17   5
  13Q GAIN WILD-TYPE 401  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     17    5
  13Q GAIN WILD-TYPE  401   73
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               17                401
  1                5                 73
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5  17
  13Q GAIN WILD-TYPE 184 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   17
  13Q GAIN WILD-TYPE  184  322
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                5                184
  MALE                 17                322
[1] 2 2
[1] FALSE
D25V8, continuous
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B0-4838         TCGA-B4-5377         TCGA-B4-5378 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4143         TCGA-B8-4622 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B8-5158         TCGA-CJ-6028         TCGA-CZ-4854 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4860 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5465 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5575 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-5576         TCGA-DV-A4VX         TCGA-DV-A4VZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-EU-5904         TCGA-EU-5905 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EU-5906         TCGA-EU-5907         TCGA-G6-A8L6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-G6-A8L8         TCGA-T7-A92I 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V9, continuous
D25V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       1                         0    21
  13Q GAIN WILD-TYPE     7                        56   436
D25V11, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 56
  WHITE                                   21                436
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3  13
  13Q GAIN WILD-TYPE  23 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3   13
  13Q GAIN WILD-TYPE   23  337
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               13                337
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     7   9
  14Q GAIN WILD-TYPE 344 166
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                510 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                166 
$`14Q GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4688 TCGA-B0-4696 
       38.47        43.20       112.08        94.19         3.32        28.47 
TCGA-B0-4699 TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4770 TCGA-BP-4799 TCGA-BP-4994 
        3.62        74.17        31.89        10.82        37.25        43.00 
TCGA-CJ-4901 TCGA-CJ-6028 TCGA-CZ-4865 TCGA-CZ-5460 
       47.67        53.42         5.46        94.45 

$`14Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        1.38        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       36.39        10.98        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         6.90        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.74        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95       115.00        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       27.65        39.45       109.84        50.24        56.35        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       53.26       118.85        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 
       18.44        79.63        90.54        91.69        55.33        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.32               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            112.08             149.16 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            40.735             38.415 
[1] "3.3 - 112.1 (40.7)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.7"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         5        2         4        5
  14Q GAIN WILD-TYPE     258       55       121       78
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  5                258
  STAGE II                 2                 55
  STAGE III                4                121
  STAGE IV                 5                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED     5   2   6   3
  14Q GAIN WILD-TYPE 263  67 174   8
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                5                263
  T2                2                 67
  T3                6                174
  T4                3                  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"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     9   0
  14Q GAIN WILD-TYPE 225  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9    0
  14Q GAIN WILD-TYPE  225   17
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                9                225
  1                0                 17
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    12   4
  14Q GAIN WILD-TYPE 406  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     12    4
  14Q GAIN WILD-TYPE  406   74
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               12                406
  1                4                 74
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  11
  14Q GAIN WILD-TYPE 184 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   11
  14Q GAIN WILD-TYPE  184  328
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                5                184
  MALE                 11                328
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CZ-4854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4860 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4VX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DV-A4VZ         TCGA-DV-A4W0         TCGA-EU-5904 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-T7-A92I 
"14Q GAIN WILD-TYPE" 
D26V9, continuous
D26V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         1    15
  14Q GAIN WILD-TYPE     8                        55   442
D26V11, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   15                442
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  11
  14Q GAIN WILD-TYPE  26 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   11
  14Q GAIN WILD-TYPE   26  339
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               11                339
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    18   8
  15Q GAIN WILD-TYPE 333 167
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                500 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                167 
$`15Q GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3430 TCGA-AK-3433 
       38.47        24.16        43.20        20.28        15.78       112.08 
TCGA-B0-4688 TCGA-B0-5081 TCGA-B4-5838 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4337 
        3.32        11.90         5.46        61.78        54.90         0.07 
TCGA-BP-4342 TCGA-BP-4803 TCGA-BP-4969 TCGA-BP-4994 TCGA-BP-5173 TCGA-BP-5185 
       74.17         6.71        58.98        43.00         1.74        37.22 
TCGA-CJ-4871 TCGA-CJ-4875 TCGA-CJ-4897 TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4866 
       79.66       116.84       109.84        85.78        66.31        61.41 
TCGA-CZ-5456 TCGA-CZ-5460 
       79.63        94.45 

$`15Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.63        74.76        53.29        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      117.80        73.08       109.41        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       94.19        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       82.45        72.89        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 
       70.52        20.94        43.30        11.24         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.10         0.85         0.53         4.64         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4325 
       89.36        23.05        77.03        62.24        64.27        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       21.21        15.16        93.99        18.48        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       13.15        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10         6.35        79.30        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95       115.00        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
       58.95        11.05        21.24        83.97        49.25        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       74.27        75.06        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83         5.39        73.18        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66       107.54        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       55.33        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.07               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            116.84             149.16 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             49.05              37.94 
[1] "0.1 - 116.8 (49.0)" "0.1 - 149.2 (37.9)"
[1] "hr=" "1.2"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED        10        4         6        6
  15Q GAIN WILD-TYPE     253       53       119       77
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                 10                253
  STAGE II                 4                 53
  STAGE III                6                119
  STAGE IV                 6                 77
[1] 4 2
[1] TRUE
[1] "dimension of 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    10   4  11   1
  15Q GAIN WILD-TYPE 258  65 169  10
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               10                258
  T2                4                 65
  T3               11                169
  T4                1                 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"
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    10   2
  15Q GAIN WILD-TYPE 224  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10    2
  15Q GAIN WILD-TYPE  224   15
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               10                224
  1                2                 15
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    21   5
  15Q GAIN WILD-TYPE 397  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     21    5
  15Q GAIN WILD-TYPE  397   73
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               21                397
  1                5                 73
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     8  18
  15Q GAIN WILD-TYPE 181 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8   18
  15Q GAIN WILD-TYPE  181  321
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                8                181
  MALE                 18                321
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         1    25
  15Q GAIN WILD-TYPE     8                        55   432
D27V11, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   25                432
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  16
  15Q GAIN WILD-TYPE  25 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   16
  15Q GAIN WILD-TYPE   25  334
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               16                334
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    73  34
  16P GAIN WILD-TYPE 278 141
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               107                419 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                34                141 
$`16P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3382 
       24.16        37.15        38.47        42.97        24.16        18.87 
TCGA-A3-3387 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4707 
       20.28       112.08        94.19        83.21         3.62        19.73 
TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       43.96        46.59        78.44        27.42        53.88         6.71 
TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5113 TCGA-B0-5400 
       43.30        11.90        90.87        52.54        38.63        56.98 
TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B2-4098 TCGA-B2-5639 
       42.41       129.67        85.78        86.47         1.68        32.98 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4621 
        5.10         0.85         0.53         5.46        25.55        25.91 
TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 
       29.88         4.93       101.06        93.34         0.43        89.36 
TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4756 
       61.78         0.07        93.99        31.89        11.31        12.30 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4803 
       13.15        68.38        11.64        15.78        10.98         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 
       47.97        71.41         6.74        58.98        48.89        49.38 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5173 
       14.93        36.07         3.88        43.00        45.07         1.74 
TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4636 TCGA-CJ-4644 
       30.64        62.86        19.82        34.95        63.25        11.05 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 
       79.66        74.27       116.84       113.46        63.98       109.84 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 
       47.67        51.25        49.28       131.08        72.00       133.71 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5581 TCGA-CW-5588 
       22.32       122.83        62.10        53.42        92.02        66.31 
TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5454 
       74.66        69.21        58.75         6.77        61.41        23.74 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5984 
       79.63        90.54        94.45         2.40        31.10        67.96 
TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-EU-5905 
       12.16        37.15        53.46        81.21         3.91 

$`16P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.08        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        62.01        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 
       52.93        45.53        29.92        18.44        88.37        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       43.20        55.76        20.71        18.64        28.31        65.52 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68        68.61       109.51        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       78.64        40.01        49.28        94.29        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         1.38        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 
       10.09        68.71        40.70        45.30        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 
       36.85        70.52        20.94        11.24         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 
       52.08        15.95        62.89        90.48        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       19.30        66.05        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 
       38.43        48.82        46.39       111.52       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       15.78        70.68       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 
       89.49        91.46       126.05        32.61        35.90        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        24.82        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
       12.00         5.75         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       34.39        14.30        27.29        17.06         1.74         8.42 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 
       94.72        90.28        32.61        99.85        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       44.94        12.23        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       13.51        56.91        60.95        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
       36.39        37.25        36.95         6.94        87.45        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22        61.51        57.40        14.24 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4983 
       45.50         6.90        47.11        53.65        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 
       31.30        25.81        36.95        27.22        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        5.82        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        6.35        79.30        74.20        52.27         9.63        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        44.55        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
      105.37        58.95        21.24        83.97        49.25        10.72 
TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       64.18        30.64        51.52       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       24.66        27.65        39.45        50.24        56.35        49.97 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
      108.56        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
        3.06         4.57        18.81       129.40        25.71        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       25.25        18.15        73.35        67.00        53.26       118.85 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 
       75.58        62.66       119.64         7.36        64.57        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
        5.39        85.78        73.18        78.18         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       47.08        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 
       63.42        58.82        79.53        18.44        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
        1.94        12.69        80.19        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 
       22.78        62.63        13.28        45.96        65.88        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       66.28        56.84        23.90        12.00        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.07               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            133.71             149.16 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             43.96              37.25 
[1] "0.1 - 133.7 (44.0)" "0.1 - 149.2 (37.2)"
[1] "hr=" "1.2"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED        47        8        32       20
  16P GAIN WILD-TYPE     216       49        93       63
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                 47                216
  STAGE II                 8                 49
  STAGE III               32                 93
  STAGE IV                20                 63
[1] 4 2
[1] TRUE
[1] "dimension of 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    47  10  47   3
  16P GAIN WILD-TYPE 221  59 133   8
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               47                221
  T2               10                 59
  T3               47                133
  T4                3                  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"
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    51   1
  16P GAIN WILD-TYPE 183  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     51    1
  16P GAIN WILD-TYPE  183   16
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               51                183
  1                1                 16
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    85  18
  16P GAIN WILD-TYPE 333  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     85   18
  16P GAIN WILD-TYPE  333   60
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               85                333
  1               18                 60
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    36  71
  16P GAIN WILD-TYPE 153 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     36   71
  16P GAIN WILD-TYPE  153  268
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               36                153
  MALE                 71                268
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 11 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B8-5550         TCGA-G6-A8L7         TCGA-MM-A563 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MM-A84U         TCGA-T7-A92I 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         7    99
  16P GAIN WILD-TYPE     7                        49   358
D28V11, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                7                 49
  WHITE                                   99                358
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     5  65
  16P GAIN WILD-TYPE  21 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   65
  16P GAIN WILD-TYPE   21  285
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 21
  NOT HISPANIC OR LATINO               65                285
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    68  31
  16Q GAIN WILD-TYPE 283 144
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                99                427 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                144 
$`16Q GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3433 
       24.16        38.47        42.97        18.87        20.28       112.08 
TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4811 
       94.19        83.21         3.62        19.73        43.96        46.59 
TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5102 
       78.44        27.42        53.88        43.30        11.90        90.87 
TCGA-B0-5106 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       52.54        38.63        56.98       129.67        85.78        86.47 
TCGA-B2-4098 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4621 
        1.68         5.10         0.85         5.46        25.55        25.91 
TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 
       29.88         4.93       101.06        93.34         0.43        89.36 
TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4756 
       61.78         0.07        93.99        31.89        11.31        12.30 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4803 
       13.15        68.38        11.64        15.78        10.98         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 
       47.97        71.41         6.74        58.98        48.89        49.38 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5173 TCGA-BP-5175 
       14.93        36.07         3.88        43.00         1.74        30.64 
TCGA-BP-5178 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4636 TCGA-CJ-4644 TCGA-CJ-4871 
       62.86        19.82        34.95        63.25        11.05        79.66 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 
       74.27       116.84       113.46        63.98       109.84        47.67 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5679 
       51.25        49.28       131.08        72.00       133.71        22.32 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5581 TCGA-CW-5588 TCGA-CW-5591 
      122.83        62.10        53.42        92.02        66.31        74.66 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5457 
       69.21        58.75         6.77        61.41        79.63        90.54 
TCGA-CZ-5460 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-5568 TCGA-DV-5573 
       94.45         2.40        31.10        67.96        12.16        37.15 
TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-EU-5905 
       53.46        81.21         3.91 

$`16Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.99        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       12.13        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 
        2.53         3.48        28.47        19.00         1.38        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       58.45        15.72         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        68.71        40.70        45.30 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       90.48        30.48        58.59        19.30        66.05        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       111.52       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
      126.05        32.61        35.90        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        5.75         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       34.39        14.30        27.29        17.06         1.74         8.42 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 
       94.72        90.28        32.61        99.85        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       44.94        12.23        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       13.51        56.91        60.95        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
       36.39        37.25        36.95         6.94        87.45        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22        61.51        57.40        14.24 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4983 
       45.50         6.90        47.11        53.65        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 
       31.30        25.81        36.95        27.22        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       48.10         6.35        79.30        74.20        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 
       13.41        24.62        33.47        44.55        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61       105.37        58.95        21.24        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       10.72        75.06        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 
       57.83        64.18        30.64        51.52       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       49.97       108.56        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5677 
       45.14         3.06         4.57        18.81       129.40        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.87        25.25        18.15        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
      118.85        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 
       81.83         5.39        85.78        73.18        78.18         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
        0.59        47.08        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       91.69        55.33        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       84.30        22.52         1.94        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ 
       65.88        11.67        66.28        56.84        23.90        12.00 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.07               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            133.71             149.16 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             47.97              37.25 
[1] "0.1 - 133.7 (48.0)" "0.1 - 149.2 (37.2)"
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED        44        8        31       16
  16Q GAIN WILD-TYPE     219       49        94       67
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                 44                219
  STAGE II                 8                 49
  STAGE III               31                 94
  STAGE IV                16                 67
[1] 4 2
[1] TRUE
[1] "dimension of 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    44   8  45   2
  16Q GAIN WILD-TYPE 224  61 135   9
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               44                224
  T2                8                 61
  T3               45                135
  T4                2                  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"
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    48   1
  16Q GAIN WILD-TYPE 186  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     48    1
  16Q GAIN WILD-TYPE  186   16
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               48                186
  1                1                 16
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    80  15
  16Q GAIN WILD-TYPE 338  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     80   15
  16Q GAIN WILD-TYPE  338   63
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               80                338
  1               15                 63
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    35  64
  16Q GAIN WILD-TYPE 154 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     35   64
  16Q GAIN WILD-TYPE  154  275
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               35                154
  MALE                 64                275
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 11 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B8-5550         TCGA-G6-A8L7         TCGA-MM-A563 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MM-A84U         TCGA-T7-A92I 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         7    91
  16Q GAIN WILD-TYPE     7                        49   366
D29V11, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                7                 49
  WHITE                                   91                366
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5  59
  16Q GAIN WILD-TYPE  21 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   59
  16Q GAIN WILD-TYPE   21  291
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 21
  NOT HISPANIC OR LATINO               59                291
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    18   8
  17P GAIN WILD-TYPE 333 167
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                26                500 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                167 
$`17P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3363 TCGA-AK-3453 TCGA-B0-4696 TCGA-B0-5102 
       24.16        38.47        10.49        83.21        28.47        90.87 
TCGA-B0-5109 TCGA-B4-5838 TCGA-B8-4621 TCGA-B8-5551 TCGA-BP-4176 TCGA-BP-4177 
       19.30         5.46        25.91         0.53        64.27        54.90 
TCGA-BP-4756 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5185 
       12.30        13.15        68.38        31.30         1.74        37.22 
TCGA-BP-5200 TCGA-CJ-4873 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CZ-4866 TCGA-CZ-5469 
       34.95        74.27        47.67        49.28        61.41        31.10 
TCGA-EU-5905 TCGA-T7-A92I 
        3.91        11.70 

$`17P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.99        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        82.32        51.25        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
      112.08        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       78.64        40.01        49.28        94.29        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.48        52.54        30.48        58.59        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        5.75         5.10         0.85         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4326 
       23.05        77.03        62.24        61.78        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 
       11.31        12.33        33.99        31.33        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
       53.65        14.93        36.07        33.34        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10         6.35        79.30        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
      109.84        50.24        56.35        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        81.21        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC 
       23.01        16.37 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.53               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             90.87             149.16 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            31.200             38.845 
[1] "0.5 - 90.9 (31.2)"  "0.1 - 149.2 (38.8)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED        15        4         6        1
  17P GAIN WILD-TYPE     248       53       119       82
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                 15                248
  STAGE II                 4                 53
  STAGE III                6                119
  STAGE IV                 1                 82
[1] 4 2
[1] TRUE
[1] "dimension of 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    15   4   7   0
  17P GAIN WILD-TYPE 253  65 173  11
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               15                253
  T2                4                 65
  T3                7                173
  T4                0                 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"
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    10   2
  17P GAIN WILD-TYPE 224  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     10    2
  17P GAIN WILD-TYPE  224   15
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               10                224
  1                2                 15
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    25   0
  17P GAIN WILD-TYPE 393  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     25    0
  17P GAIN WILD-TYPE  393   78
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               25                393
  1                0                 78
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     9  17
  17P GAIN WILD-TYPE 180 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9   17
  17P GAIN WILD-TYPE  180  322
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                9                180
  MALE                 17                322
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 19 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-5158         TCGA-B8-5164 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B8-5550         TCGA-B8-A54E         TCGA-B8-A54F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-DV-A4VX 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MM-A563 
"17P GAIN WILD-TYPE" 
D30V10, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 11 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B8-5550         TCGA-DV-A4W0         TCGA-G6-A8L7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MM-A563         TCGA-MM-A84U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       2                         4    20
  17P GAIN WILD-TYPE     6                        52   437
D30V11, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                4                 52
  WHITE                                   20                437
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  15
  17P GAIN WILD-TYPE  26 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   15
  17P GAIN WILD-TYPE   26  335
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               15                335
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    22  11
  17Q GAIN WILD-TYPE 329 164
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                33                493 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                11                164 
$`17Q GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3363 TCGA-AK-3453 TCGA-B0-4707 TCGA-B0-5102 
       24.16        38.47        10.49        83.21        19.73        90.87 
TCGA-B0-5109 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4621 TCGA-B8-5551 
       19.30         0.53         5.46        23.31        25.91         0.53 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4768 
       64.27        54.90         0.07        12.30        72.59        13.15 
TCGA-BP-4781 TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5200 
       68.38        31.30         1.74        38.30        37.22        34.95 
TCGA-CJ-4873 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5469 
       74.27        47.67        49.28         6.77        61.41        31.10 
TCGA-EU-5905 TCGA-G6-A8L7 TCGA-T7-A92I 
        3.91        70.13        11.70 

$`17Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.99        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        82.32        51.25        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
      112.08        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       78.64        40.01        49.28        94.29        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        5.98         2.14        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.48        52.54        30.48        58.59        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         5.10         0.85         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.55        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       62.24        61.78        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
       62.07        80.68        37.25        21.21        15.16        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       44.94        12.23        31.89        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       31.33        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       60.59        13.51        56.91        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       44.55        31.27         0.95       115.00        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       10.72        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        50.24        56.35        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
      108.56        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        81.21        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       10.29        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC 
       16.37 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             90.87             149.16 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             31.10              39.16 
[1] "0.1 - 90.9 (31.1)"  "0.1 - 149.2 (39.2)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED        19        4         7        3
  17Q GAIN WILD-TYPE     244       53       118       80
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                 19                244
  STAGE II                 4                 53
  STAGE III                7                118
  STAGE IV                 3                 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"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED    19   4   9   1
  17Q GAIN WILD-TYPE 249  65 171  10
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               19                249
  T2                4                 65
  T3                9                171
  T4                1                 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"
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    14   2
  17Q GAIN WILD-TYPE 220  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     14    2
  17Q GAIN WILD-TYPE  220   15
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               14                220
  1                2                 15
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    29   2
  17Q GAIN WILD-TYPE 389  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     29    2
  17Q GAIN WILD-TYPE  389   76
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               29                389
  1                2                 76
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    13  20
  17Q GAIN WILD-TYPE 176 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     13   20
  17Q GAIN WILD-TYPE  176  319
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               13                176
  MALE                 20                319
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 10 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B8-5550         TCGA-DV-A4W0         TCGA-MM-A563 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MM-A84U 
"17Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       2                         5    26
  17Q GAIN WILD-TYPE     6                        51   431
D31V11, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                5                 51
  WHITE                                   26                431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  19
  17Q GAIN WILD-TYPE  26 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   19
  17Q GAIN WILD-TYPE   26  331
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               19                331
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    21   4
  18P GAIN WILD-TYPE 330 171
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                501 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                171 
$`18P GAIN MUTATED`
TCGA-A3-3308 TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-B0-4710 
        0.53        38.47        43.20        18.87       112.08        57.70 
TCGA-B0-5113 TCGA-B0-5693 TCGA-B2-5633 TCGA-B4-5838 TCGA-BP-4177 TCGA-BP-4342 
       38.63       133.94        31.66         5.46        54.90        74.17 
TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4789 TCGA-BP-4992 TCGA-CJ-4635 TCGA-CJ-4872 
       31.89        13.15        48.95        16.47        46.55        10.72 
TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5585 TCGA-CZ-5457 
      109.84        49.18        64.57        81.83        85.78        90.54 
TCGA-CZ-5467 
        2.40 

$`18P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82        47.21        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.99        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        2.14        19.73        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 
       35.90         1.68        31.96        21.30        31.30        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.85         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 
       23.05        77.03        62.24        61.78        64.27        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 
       62.86        54.77        49.08        44.94        12.23        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4790 
       56.91        68.38        11.64        60.95        15.78        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 
       25.81        36.95        27.22         3.88        46.45         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.74        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95       115.00 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      105.37        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       79.66        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.25       108.56        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02         5.39        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66       107.54        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       69.96        84.30        22.52         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.53               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            133.94             149.16 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             46.55              37.58 
[1] "0.5 - 133.9 (46.5)" "0.1 - 149.2 (37.6)"
[1] "hr=" "2.4"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED        13        2         7        3
  18P GAIN WILD-TYPE     250       55       118       80
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                 13                250
  STAGE II                 2                 55
  STAGE III                7                118
  STAGE IV                 3                 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"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED    13   2  10   0
  18P GAIN WILD-TYPE 255  67 170  11
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               13                255
  T2                2                 67
  T3               10                170
  T4                0                 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"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    12   1
  18P GAIN WILD-TYPE 222  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     12    1
  18P GAIN WILD-TYPE  222   16
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               12                222
  1                1                 16
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    23   2
  18P GAIN WILD-TYPE 395  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     23    2
  18P GAIN WILD-TYPE  395   76
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               23                395
  1                2                 76
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    13  12
  18P GAIN WILD-TYPE 176 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     13   12
  18P GAIN WILD-TYPE  176  327
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               13                176
  MALE                 12                327
[1] 2 2
[1] FALSE
D32V8, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 51 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5843 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4143         TCGA-B8-4622 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B8-5158         TCGA-CJ-6028         TCGA-CZ-4854 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4860 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-5458         TCGA-CZ-5465         TCGA-CZ-5469 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-5982         TCGA-DV-5565         TCGA-DV-5566 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-5576         TCGA-DV-A4VX         TCGA-DV-A4VZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-EU-5904         TCGA-EU-5905 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EU-5906         TCGA-EU-5907         TCGA-G6-A8L6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-G6-A8L8         TCGA-T7-A92I 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D32V9, continuous
D32V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         1    24
  18P GAIN WILD-TYPE     8                        55   433
D32V11, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   24                433
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  15
  18P GAIN WILD-TYPE  24 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   15
  18P GAIN WILD-TYPE   24  335
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               15                335
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    20   5
  18Q GAIN WILD-TYPE 331 170
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                25                501 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                170 
$`18Q GAIN MUTATED`
TCGA-A3-3308 TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-B0-4707 
        0.53        38.47        43.20        18.87       112.08        19.73 
TCGA-B0-4710 TCGA-B0-5113 TCGA-B0-5693 TCGA-B2-5633 TCGA-B4-5838 TCGA-BP-4177 
       57.70        38.63       133.94        31.66         5.46        54.90 
TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4789 TCGA-BP-4992 TCGA-CJ-4635 
       74.17        31.89        13.15        48.95        16.47        46.55 
TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5585 TCGA-CZ-5457 
      109.84        49.18        64.57        81.83        85.78        90.54 
TCGA-CZ-5467 
        2.40 

$`18Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82        47.21        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.99        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       52.54        30.48        58.59        19.30        66.05        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5694 
       56.98        42.41       111.52       112.80       129.67        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        0.53         4.64         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       15.16         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        60.95        15.78        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 
       36.95        27.22         3.88        46.45         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.74        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       44.55        34.95        31.27         0.95       115.00        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.25       108.56        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02         5.39        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66       107.54        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       69.96        84.30        22.52         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.53               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            133.94             149.16 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             46.55              37.58 
[1] "0.5 - 133.9 (46.5)" "0.1 - 149.2 (37.6)"
[1] "hr=" "2"  
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED        12        2         8        3
  18Q GAIN WILD-TYPE     251       55       117       80
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                 12                251
  STAGE II                 2                 55
  STAGE III                8                117
  STAGE IV                 3                 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"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED    12   2  11   0
  18Q GAIN WILD-TYPE 256  67 169  11
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               12                256
  T2                2                 67
  T3               11                169
  T4                0                 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"
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    11   1
  18Q GAIN WILD-TYPE 223  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     11    1
  18Q GAIN WILD-TYPE  223   16
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               11                223
  1                1                 16
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    23   2
  18Q GAIN WILD-TYPE 395  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     23    2
  18Q GAIN WILD-TYPE  395   76
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               23                395
  1                2                 76
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    13  12
  18Q GAIN WILD-TYPE 176 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     13   12
  18Q GAIN WILD-TYPE  176  327
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               13                176
  MALE                 12                327
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5843 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4143         TCGA-B8-4622 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B8-5158         TCGA-CJ-6028         TCGA-CZ-4854 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4860 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-5458         TCGA-CZ-5465         TCGA-CZ-5469 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-5982         TCGA-DV-5565         TCGA-DV-5566 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-5576         TCGA-DV-A4VX         TCGA-DV-A4VZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-EU-5904         TCGA-EU-5905 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EU-5906         TCGA-EU-5907         TCGA-G6-A8L6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-G6-A8L8         TCGA-T7-A92I 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D33V9, continuous
D33V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         1    24
  18Q GAIN WILD-TYPE     8                        55   433
D33V11, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   24                433
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  15
  18Q GAIN WILD-TYPE  24 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   15
  18Q GAIN WILD-TYPE   24  335
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               15                335
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    33  18
  19P GAIN WILD-TYPE 318 157
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                51                475 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                18                157 
$`19P GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 
       38.47        43.20        18.87       112.08        94.19        83.21 
TCGA-B0-4688 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4822 TCGA-B0-4844 
        3.32         3.62        57.70        46.59        36.53        10.29 
TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5102 TCGA-B0-5109 TCGA-B4-5832 TCGA-B4-5838 
        7.30        10.95        90.87        19.30         5.10         5.46 
TCGA-B8-4143 TCGA-BP-4166 TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4768 
       23.31         0.43        74.17        31.89        11.31        13.15 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4994 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5198 
        6.74        58.98        43.00        62.86        37.22        19.82 
TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4897 TCGA-CJ-4907 
       34.95        46.55        79.66        74.27       109.84        49.28 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CW-5591 TCGA-CZ-4854 
      131.08       133.71       122.83        53.42        74.66        46.16 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 
       61.41        79.63        90.54        94.45        10.85        69.96 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
       31.10        67.96         3.91 

$`19P GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.64        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61       109.51        46.78        48.36        78.64        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       49.28        94.29        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       82.45        72.89        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 
       65.10         7.82         5.98         2.14        19.73        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 
        6.64         3.25        58.45        15.72         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.52        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        18.51        15.09         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       58.59        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
      111.52       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         5.75         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.36         0.23        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.74        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       30.64        52.27         9.63        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       31.27         0.95       115.00        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        10.72        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       47.67        49.97        51.25       108.56        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00       129.40        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       18.15        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
      107.54        63.39        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
       79.53        23.74        18.44        91.69        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       21.76        84.30        22.52         2.40         1.94        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.43               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            133.71             149.16 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             46.16              37.58 
[1] "0.4 - 133.7 (46.2)" "0.1 - 149.2 (37.6)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED        15        7        13       16
  19P GAIN WILD-TYPE     248       50       112       67
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                 15                248
  STAGE II                 7                 50
  STAGE III               13                112
  STAGE IV                16                 67
[1] 4 2
[1] TRUE
[1] "dimension of 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    16   7  26   2
  19P GAIN WILD-TYPE 252  62 154   9
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               16                252
  T2                7                 62
  T3               26                154
  T4                2                  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"
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    22   3
  19P GAIN WILD-TYPE 212  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     22    3
  19P GAIN WILD-TYPE  212   14
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               22                212
  1                3                 14
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    36  15
  19P GAIN WILD-TYPE 382  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     36   15
  19P GAIN WILD-TYPE  382   63
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               36                382
  1               15                 63
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    14  37
  19P GAIN WILD-TYPE 175 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     14   37
  19P GAIN WILD-TYPE  175  302
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               14                175
  MALE                 37                302
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
D34V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         1    50
  19P GAIN WILD-TYPE     8                        55   407
D34V11, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   50                407
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  33
  19P GAIN WILD-TYPE  23 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   33
  19P GAIN WILD-TYPE   23  317
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               33                317
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    35  22
  19Q GAIN WILD-TYPE 316 153
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                469 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                153 
$`19Q GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3436 
       38.47        34.29        43.20        18.87       112.08       109.51 
TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4710 
       94.19        83.21         3.32         3.62        19.73        57.70 
TCGA-B0-4811 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5084 
       46.59        40.44        36.53        10.09        10.29         7.30 
TCGA-B0-5094 TCGA-B0-5102 TCGA-B0-5109 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 
       10.95        90.87        19.30         5.10         5.46        23.31 
TCGA-BP-4166 TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4967 
        0.43        74.17        31.89        11.31        13.15         6.74 
TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5198 
       58.98        31.30        43.00        62.86        37.22        19.82 
TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4897 TCGA-CJ-4907 
       34.95        46.55        79.66        74.27       109.84        49.28 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CW-5591 TCGA-CZ-4854 
      131.08       133.71       122.83        53.42        74.66        46.16 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 
       61.41        79.63        90.54        94.45        10.85        69.96 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
       31.10        67.96         3.91 

$`19Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 
       36.36        38.99        37.38        48.82        62.01        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       15.72         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       16.77         6.02        14.93        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        10.52        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
       11.90        25.32        18.51        15.09         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        58.59        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67        12.00         5.75         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        0.53         4.64         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       61.51        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.74        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       30.64        52.27         9.63        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       31.27         0.95       115.00        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        10.72        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       47.67        49.97        51.25       108.56        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00       129.40        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       18.15        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
      107.54        63.39        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
       79.53        23.74        18.44        91.69        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       21.76        84.30        22.52         2.40         1.94        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.43               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            133.71             149.16 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              43.0               38.3 
[1] "0.4 - 133.7 (43.0)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED        16        7        16       18
  19Q GAIN WILD-TYPE     247       50       109       65
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                 16                247
  STAGE II                 7                 50
  STAGE III               16                109
  STAGE IV                18                 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"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED    17   9  29   2
  19Q GAIN WILD-TYPE 251  60 151   9
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               17                251
  T2                9                 60
  T3               29                151
  T4                2                  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"
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    25   3
  19Q GAIN WILD-TYPE 209  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     25    3
  19Q GAIN WILD-TYPE  209   14
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               25                209
  1                3                 14
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    40  17
  19Q GAIN WILD-TYPE 378  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     40   17
  19Q GAIN WILD-TYPE  378   61
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               40                378
  1               17                 61
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    16  41
  19Q GAIN WILD-TYPE 173 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     16   41
  19Q GAIN WILD-TYPE  173  298
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               16                173
  MALE                 41                298
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         1    55
  19Q GAIN WILD-TYPE     7                        55   402
D35V11, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   55                402
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3  38
  19Q GAIN WILD-TYPE  23 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   38
  19Q GAIN WILD-TYPE   23  312
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               38                312
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    68  44
  20P GAIN WILD-TYPE 283 131
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               112                414 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                44                131 
$`20P GAIN MUTATED`
TCGA-3Z-A93Z TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3325 TCGA-A3-3358 
       12.66         0.53        24.16        49.08        38.47        42.97 
TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3429 
       24.16        43.20        18.87        65.52       117.80       109.41 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 
      112.08        94.19        78.64        83.21         3.32         1.41 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4811 
        1.38         3.62        65.10        19.73        43.96        46.59 
TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4844 
       52.21         6.02        36.53        10.09        40.70        10.29 
TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5106 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 
       29.03        10.95        52.54        19.30        38.63        41.88 
TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
        5.10         5.46        25.55        25.91        50.14        20.91 
TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4176 
       27.02         0.53         4.93         0.43        89.36        64.27 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4761 
        0.07        93.99        74.17        62.86        31.89         5.98 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 
       13.15        68.38        15.78        10.98        37.25         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4983 TCGA-BP-4985 
       47.97        71.41         6.74        58.98        46.45        31.30 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5173 TCGA-BP-5175 
       16.47        43.00        36.23        28.87         1.74        30.64 
TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 
       62.86        37.22        31.79        19.82        34.95        46.55 
TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 
       11.05        79.66        10.72        74.27       116.84        66.21 
TCGA-CJ-4882 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 
       61.91       109.84        47.67        49.97        51.25        49.28 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CW-5588 TCGA-CW-5591 
      131.08       133.71        22.32       122.83        66.31        74.66 
TCGA-CW-6087 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 
        1.35        46.16        47.08        69.21         6.77        14.66 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5468 
       61.41        79.63        94.45        10.85        69.96         1.94 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-A4VX TCGA-EU-5905 
       31.10        67.96        53.46         3.91 

$`20P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 
       11.90        36.82        47.21        39.16        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       49.58        48.59        36.36        38.99        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       62.01        34.29        31.07         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       29.92        18.44        88.37        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       28.70        74.63        74.76        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
       73.08        15.78        73.68        68.61       109.51        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       48.36        40.01        49.28        94.29        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       16.77        40.44        14.93        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       68.71        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       10.52        65.29        39.45        26.07         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        18.51        15.09         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 
       52.08        15.95        62.89        90.87        90.48        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       58.59        66.05        52.73        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        31.66        24.82        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
       12.00         5.75         0.85         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       45.37        17.19        23.74         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 
       90.28       101.06        93.34        32.61        99.85        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        61.78        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       15.16        18.48        52.24        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98        77.62        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        11.64        60.95        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
       20.38        36.39        36.95         6.94        87.45        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22        61.51        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       14.93        36.07        33.34        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        3.88        46.45         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       48.10         6.35        79.30        74.20        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       74.40        49.15        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       33.47        44.55        31.27         0.95       115.00        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 
       58.95        21.24        83.97        49.25        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       71.87        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       39.45        50.24        56.35       108.56        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
       72.00       129.40        25.71        18.87        25.25        18.15 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 
       81.83         5.39        85.78        73.18        78.18       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 
       83.90       103.43        18.77        25.45         0.59        58.75 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
      107.54        63.39        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 
       10.22        21.76        84.30        22.52         2.40        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       66.28        56.84        23.90        12.00        81.21        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            133.71             149.16 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            38.550             38.415 
[1] "0.1 - 133.7 (38.5)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.3"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED        34       12        38       28
  20P GAIN WILD-TYPE     229       45        87       55
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 34                229
  STAGE II                12                 45
  STAGE III               38                 87
  STAGE IV                28                 55
[1] 4 2
[1] TRUE
[1] "dimension of 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    35  13  58   6
  20P GAIN WILD-TYPE 233  56 122   5
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               35                233
  T2               13                 56
  T3               58                122
  T4                6                  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"
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    49   5
  20P GAIN WILD-TYPE 185  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     49    5
  20P GAIN WILD-TYPE  185   12
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               49                185
  1                5                 12
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    84  26
  20P GAIN WILD-TYPE 334  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     84   26
  20P GAIN WILD-TYPE  334   52
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               84                334
  1               26                 52
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    24  88
  20P GAIN WILD-TYPE 165 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     24   88
  20P GAIN WILD-TYPE  165  251
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               24                165
  MALE                 88                251
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 10 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3451 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5550         TCGA-DV-A4W0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563         TCGA-MM-A84U 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-T7-A92I 
"20P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       1                         8   103
  20P GAIN WILD-TYPE     7                        48   354
D36V11, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                8                 48
  WHITE                                  103                354
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     3  71
  20P GAIN WILD-TYPE  23 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   71
  20P GAIN WILD-TYPE   23  279
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               71                279
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    69  46
  20Q GAIN WILD-TYPE 282 129
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               115                411 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                46                129 
$`20Q GAIN MUTATED`
TCGA-3Z-A93Z TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3325 
       12.66         0.53        24.16        49.08        37.15        38.47 
TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 
       52.93        42.97        24.16        43.20        18.87        65.52 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3453 
      117.80       109.41       112.08        94.19        78.64        83.21 
TCGA-B0-4690 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4707 TCGA-B0-4712 
        1.41         1.38         3.62        65.10        19.73        43.96 
TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 
       46.59        52.21         6.02        40.44        36.53        10.09 
TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5106 TCGA-B0-5109 
       40.70        10.29        29.03        10.95        52.54        19.30 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4621 
       38.63        41.88         5.10         5.46        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4166 
       50.14        20.91        27.02         0.53         4.93         0.43 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4343 
       89.36        64.27         0.07        93.99        74.17        62.86 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 
       31.89        11.31         5.98        13.15        68.38        15.78 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 
       10.98        37.25         6.71        47.97        71.41         6.74 
TCGA-BP-4969 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5009 
       58.98        46.45        31.30        16.47        43.00        36.23 
TCGA-BP-5010 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5191 
       28.87         1.74        30.64        62.86        37.22        31.79 
TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 
       19.82        34.95        46.55        11.05        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4897 TCGA-CJ-4901 
       74.27       116.84        66.21        61.91       109.84        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 
       49.97        51.25        49.28       131.08       133.71        22.32 
TCGA-CJ-5682 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CZ-4854 TCGA-CZ-4857 
      122.83        66.31        74.66         1.35        46.16        47.08 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5460 
       69.21         6.77        14.66        61.41        79.63        94.45 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-A4VX 
       10.85        69.96         1.94        31.10        67.96        53.46 
TCGA-EU-5905 
        3.91 

$`20Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3320 
       11.90        36.82        47.21        39.16        49.02        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       34.29        31.07         4.50        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        55.76        20.71        18.64        28.31 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3430 
       11.18        10.62       109.91        29.10        73.08        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
       73.68        68.61       109.51        46.78        48.36        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       49.28        94.29        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 
        4.57         2.53         3.48        28.47        19.00         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       15.72         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 
       14.93        54.48        29.10        78.44        68.71        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 
       27.42        53.88         6.71        56.68        10.52        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       15.09         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.87        90.48        30.48        58.59        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.85         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74         1.18         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
       17.06         1.74         8.42        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       93.34        32.61        99.85        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       61.78        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 
       62.07        80.68        37.25        21.21        15.16        18.48 
TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 
       52.24        54.77        49.08        44.94        12.23        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        5.33        61.97        60.59        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
       60.95        48.95        36.53        20.38        36.39        36.95 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        87.45        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       61.51        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 
       25.81        36.95        27.22         3.88        46.45         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       27.62        37.48        35.21        48.10         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       74.20        52.27         9.63        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 
       23.47        13.41        24.62        33.47        44.55        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61       105.37        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 
       49.25        75.06        64.27        71.87        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
      108.56        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
        3.06         4.57        18.81        72.00       129.40        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       18.87        25.25        18.15        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       73.18        78.18       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       25.45         0.59        58.75       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       90.54        91.69        55.33        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
       22.52         2.40        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        81.21        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            133.71             149.16 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             38.63              38.40 
[1] "0.1 - 133.7 (38.6)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.3"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED        35       12        40       28
  20Q GAIN WILD-TYPE     228       45        85       55
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 35                228
  STAGE II                12                 45
  STAGE III               40                 85
  STAGE IV                28                 55
[1] 4 2
[1] TRUE
[1] "dimension of 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    37  13  60   5
  20Q GAIN WILD-TYPE 231  56 120   6
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               37                231
  T2               13                 56
  T3               60                120
  T4                5                  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"
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    50   6
  20Q GAIN WILD-TYPE 184  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     50    6
  20Q GAIN WILD-TYPE  184   11
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               50                184
  1                6                 11
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    87  26
  20Q GAIN WILD-TYPE 331  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     87   26
  20Q GAIN WILD-TYPE  331   52
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               87                331
  1               26                 52
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    27  88
  20Q GAIN WILD-TYPE 162 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     27   88
  20Q GAIN WILD-TYPE  162  251
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               27                162
  MALE                 88                251
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
D37V10, continuous
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                 10 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3451 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5550         TCGA-DV-A4W0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563         TCGA-MM-A84U 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-T7-A92I 
"20Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         8   105
  20Q GAIN WILD-TYPE     6                        48   352
D37V11, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                8                 48
  WHITE                                  105                352
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3  73
  20Q GAIN WILD-TYPE  23 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   73
  20Q GAIN WILD-TYPE   23  277
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               73                277
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    31  19
  21Q GAIN WILD-TYPE 320 156
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                50                476 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                156 
$`21Q GAIN MUTATED`
TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3445 
       49.08        48.59        24.16        18.87       109.41        78.64 
TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4844 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5106 
        1.41        28.47        10.29        15.95        90.87        52.54 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5696 TCGA-B4-5832 TCGA-B8-5163 TCGA-B8-A54F 
       38.63        41.88        85.78         5.10        27.02        17.06 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 
       89.36        64.27         0.07        93.99        31.89        11.31 
TCGA-BP-4763 TCGA-BP-4781 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4995 TCGA-BP-5173 
       41.75        68.38        58.98        31.30        45.07         1.74 
TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5191 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4873 
       62.86        37.22        31.79        46.55        14.17        74.27 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4866 
      133.71        22.32       118.85        74.66        46.16        61.41 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-DV-5568 TCGA-DV-5573 
       94.45        10.85         1.94        31.10        12.16        37.15 
TCGA-DV-A4W0 TCGA-EU-5905 
       81.21         3.91 

$`21Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3324 
       24.16        49.02        37.15        49.58        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.47        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      117.80        73.08        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 
      109.51        94.19        46.78        48.36        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        4.57         2.53         3.48        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       62.89        90.48        30.48        58.59        19.30        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       15.78        70.68        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67        12.00         5.75         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G 
        0.53        34.39        14.30        27.29        29.88         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85         0.43        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       61.78        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 
       62.07        80.68        37.25        21.21        15.16        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62         5.98        44.15        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       13.15        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
       53.65        14.93        36.07        33.34        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       43.00        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       74.40        49.15        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
      115.00        63.25        73.22       106.16       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      105.37        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       79.66        10.72        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
      131.08        72.00       129.40        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66       107.54        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       91.69        55.33        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
       22.52         2.40        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       65.88        11.67        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       12.00        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.07               0.10 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            133.71             149.16 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            40.190             38.415 
[1] "0.1 - 133.7 (40.2)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED        21        3        17        9
  21Q GAIN WILD-TYPE     242       54       108       74
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                 21                242
  STAGE II                 3                 54
  STAGE III               17                108
  STAGE IV                 9                 74
[1] 4 2
[1] TRUE
[1] "dimension of 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    22   3  24   1
  21Q GAIN WILD-TYPE 246  66 156  10
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               22                246
  T2                3                 66
  T3               24                156
  T4                1                 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"
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    20   1
  21Q GAIN WILD-TYPE 214  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     20    1
  21Q GAIN WILD-TYPE  214   16
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               20                214
  1                1                 16
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    39   9
  21Q GAIN WILD-TYPE 379  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     39    9
  21Q GAIN WILD-TYPE  379   69
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               39                379
  1                9                 69
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    15  35
  21Q GAIN WILD-TYPE 174 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     15   35
  21Q GAIN WILD-TYPE  174  304
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               15                174
  MALE                 35                304
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
D38V10, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 10 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3451 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-B8-5550 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563         TCGA-MM-A84U 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-T7-A92I 
"21Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         2    48
  21Q GAIN WILD-TYPE     8                        54   409
D38V11, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 54
  WHITE                                   48                409
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3  31
  21Q GAIN WILD-TYPE  23 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3   31
  21Q GAIN WILD-TYPE   23  319
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               31                319
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    29  11
  22Q GAIN WILD-TYPE 322 164
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                40                486 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                11                164 
$`22Q GAIN MUTATED`
TCGA-A3-3306 TCGA-A3-3319 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3440 
       36.82        37.15        43.20        18.87       112.08        94.19 
TCGA-B0-4688 TCGA-B0-4699 TCGA-B0-5081 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5113 
        3.32         3.62        11.90        15.95        90.87        38.63 
TCGA-B0-5400 TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 
       56.98         5.10         5.46         0.43        61.78        64.27 
TCGA-BP-4337 TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4765 TCGA-BP-4781 
        0.07        74.17        31.89        11.31        71.80        68.38 
TCGA-BP-4975 TCGA-BP-4994 TCGA-BP-5173 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5198 
       47.11        43.00         1.74        62.86        37.22        19.82 
TCGA-BP-5200 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 
       34.95        51.25        49.28       131.08       133.71       122.83 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4860 TCGA-CZ-5984 
       66.31        74.66         6.77        67.96 

$`22Q GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.08        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.47        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
      109.51        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       82.45        72.89        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       62.89        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       48.82        46.39        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         0.85         0.53         4.64         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 
       90.28       101.06        93.34        32.61        99.85        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       23.05        77.03        62.24        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
       15.16        93.99        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
       61.97        60.59        13.51        56.91        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.90        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       30.64        52.27         9.63        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
      108.56        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
        3.06         4.57        18.81        72.00       129.40        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        22.32        25.25        18.15        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       85.78        73.18        78.18         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
        2.40         1.94        31.10        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            133.71             149.16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             43.10              38.35 
[1] "0.1 - 133.7 (43.1)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.3"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED        17        4        11        8
  22Q GAIN WILD-TYPE     246       53       114       75
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                 17                246
  STAGE II                 4                 53
  STAGE III               11                114
  STAGE IV                 8                 75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED    17   4  16   3
  22Q GAIN WILD-TYPE 251  65 164   8
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               17                251
  T2                4                 65
  T3               16                164
  T4                3                  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"
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    18   1
  22Q GAIN WILD-TYPE 216  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     18    1
  22Q GAIN WILD-TYPE  216   16
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               18                216
  1                1                 16
[1] 2 2
[1] FALSE
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    33   7
  22Q GAIN WILD-TYPE 385  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     33    7
  22Q GAIN WILD-TYPE  385   71
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               33                385
  1                7                 71
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    11  29
  22Q GAIN WILD-TYPE 178 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     11   29
  22Q GAIN WILD-TYPE  178  310
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               11                178
  MALE                 29                310
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
D39V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         1    39
  22Q GAIN WILD-TYPE     8                        55   418
D39V11, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   39                418
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  21
  22Q GAIN WILD-TYPE  25 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   21
  22Q GAIN WILD-TYPE   25  329
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               21                329
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    19  13
  XP GAIN WILD-TYPE 332 162
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               32               494 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               13               162 
$`XP GAIN MUTATED`
TCGA-A3-3346 TCGA-A3-3382 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3445 
        4.50        18.87        73.08       109.41       109.51        78.64 
TCGA-AK-3453 TCGA-B0-4827 TCGA-B0-5080 TCGA-B0-5109 TCGA-B8-A54I TCGA-BP-4162 
       83.21        29.10        11.24        19.30         4.93       101.06 
TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4770 
       61.78         0.07        93.99        11.31        12.30        10.82 
TCGA-BP-4799 TCGA-BP-4969 TCGA-BP-4989 TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 
       37.25        58.98         3.88        11.05       113.46        50.24 
TCGA-CJ-5681 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5468 
       18.15        74.66        46.16        79.63        69.96         1.94 
TCGA-DV-A4VX TCGA-EU-5905 
       53.46         3.91 

$`XP GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       34.29        31.07        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.64        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
      109.91        29.10       117.80        15.78        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 
       68.61        94.19        46.78        48.36        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       94.29        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       72.89        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       58.59        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
      111.52       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
       17.06         1.74         8.42        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 
       14.17       111.02        85.51        94.72        90.28        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        12.33        33.99        31.33 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        61.68         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 
       31.30        25.81        36.95        27.22        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.74        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61       105.37        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
       64.27        71.87        66.21        61.91        57.83        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        27.65        39.45       109.84        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       22.32        25.25       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        66.31        78.18         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        18.77        25.45         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 
       10.22        21.76        84.30        22.52         2.40        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ 
       11.67        37.15        66.28        56.84        23.90        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       81.21        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.07              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           113.46            149.16 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           41.705            38.450 
[1] "0.1 - 113.5 (41.7)" "0.1 - 149.2 (38.5)"
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED        10        4         7       11
  XP GAIN WILD-TYPE     253       53       118       72
D40V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                10               253
  STAGE II                4                53
  STAGE III               7               118
  STAGE IV               11                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"
                   vv
clus                 T1  T2  T3  T4
  XP GAIN MUTATED    10   5  16   1
  XP GAIN WILD-TYPE 258  64 164  10
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              10               258
  T2               5                64
  T3              16               164
  T4               1                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"
D40V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    19   1
  XP GAIN WILD-TYPE 215  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     19    1
  XP GAIN WILD-TYPE  215   16
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              19               215
  1               1                16
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    21   9
  XP GAIN WILD-TYPE 397  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     21    9
  XP GAIN WILD-TYPE  397   69
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              21               397
  1               9                69
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    12  20
  XP GAIN WILD-TYPE 177 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     12   20
  XP GAIN WILD-TYPE  177  319
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              12               177
  MALE                20               319
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                2                19 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3451 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621        TCGA-B8-5158 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E        TCGA-B8-A54F 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4W0        TCGA-G6-A5PC 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-MM-A563        TCGA-T7-A92I 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
D40V10, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                11 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3451        TCGA-B2-A4SR 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5550        TCGA-DV-A4W0        TCGA-G6-A8L7 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-MM-A563        TCGA-MM-A84U        TCGA-T7-A92I 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       2                         2    28
  XP GAIN WILD-TYPE     6                        54   429
D40V11, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   2                 6
  BLACK OR AFRICAN AMERICAN               2                54
  WHITE                                  28               429
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0  19
  XP GAIN WILD-TYPE  26 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   19
  XP GAIN WILD-TYPE   26  331
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              19               331
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    19  12
  XQ GAIN WILD-TYPE 332 163
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               31               495 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12               163 
$`XQ GAIN MUTATED`
TCGA-A3-3383 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3453 TCGA-B0-4827 
       28.31        73.08       109.41       109.51        83.21        29.10 
TCGA-B0-5080 TCGA-B0-5109 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4337 
       11.24        19.30         4.93       101.06        61.78         0.07 
TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4799 TCGA-BP-4969 TCGA-BP-4989 TCGA-BP-5176 
       93.99        11.31        37.25        58.98         3.88        52.27 
TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CJ-5681 TCGA-CW-5591 TCGA-CZ-4854 
       11.05       113.46        50.24        18.15        74.66        46.16 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-DV-A4VX TCGA-EU-5905 
       79.63        91.69        69.96         1.94        53.46         3.91 
TCGA-MM-A84U 
       23.01 

$`XQ GAIN WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 
       55.76        20.71        18.64        18.87        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3431 
       10.62       109.91        29.10       117.80        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
      112.08        68.61        94.19        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       40.01        49.28        94.29        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       14.93        54.48        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5084 
       36.85        70.52        20.94        43.30        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        58.59        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       21.21        15.16        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       36.95        27.22        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
        6.35        79.30         1.74        74.20        30.64         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95       115.00        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       61.91        57.83        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
      109.84        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
      133.71        25.71        18.87        22.32        25.25       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
      107.54        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 
       58.82        79.53        23.74        18.44        90.54        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       23.90        12.00        81.21        18.12         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        16.37        11.70 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           113.46            149.16 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            50.24             38.40 
[1] "0.1 - 113.5 (50.2)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED        10        4         7       10
  XQ GAIN WILD-TYPE     253       53       118       73
D41V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                10               253
  STAGE II                4                53
  STAGE III               7               118
  STAGE IV               10                73
[1] 4 2
[1] TRUE
[1] "dimension of 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    10   5  16   0
  XQ GAIN WILD-TYPE 258  64 164  11
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              10               258
  T2               5                64
  T3              16               164
  T4               0                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    17   1
  XQ GAIN WILD-TYPE 217  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     17    1
  XQ GAIN WILD-TYPE  217   16
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              17               217
  1               1                16
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    19   9
  XQ GAIN WILD-TYPE 399  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     19    9
  XQ GAIN WILD-TYPE  399   69
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              19               399
  1               9                69
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    12  19
  XQ GAIN WILD-TYPE 177 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12   19
  XQ GAIN WILD-TYPE  177  320
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              12               177
  MALE                19               320
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                20 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4W0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563        TCGA-T7-A92I 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D41V10, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                11 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5550        TCGA-DV-A4W0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-MM-A563        TCGA-T7-A92I 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       1                         3    27
  XQ GAIN WILD-TYPE     7                        53   430
D41V11, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                53
  WHITE                                  27               430
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  19
  XQ GAIN WILD-TYPE  26 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   19
  XQ GAIN WILD-TYPE   26  331
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              19               331
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    36  21
  1P LOSS WILD-TYPE 315 154
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               57               469 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               154 
$`1P LOSS MUTATED`
TCGA-A3-3313 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 
       24.16        53.29        43.20        18.64       117.80       112.08 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4698 TCGA-B0-4699 
       94.19        40.01        12.13        40.70         1.38         3.62 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5098 
       40.44        36.53        68.71        65.29        36.85        52.08 
TCGA-B0-5102 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-4098 
       90.87        52.87        42.41        73.84        32.61         1.68 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4176 TCGA-BP-4334 
        0.53         5.46        17.19         6.38        64.27        21.21 
TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4968 
       74.17        12.33        13.15        60.59        68.38        57.40 
TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5173 TCGA-BP-5201 TCGA-CJ-4640 
       25.81        43.00        37.02         1.74        31.27       114.41 
TCGA-CJ-4876 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5678 
       64.27        27.65       109.84        47.67        49.28        18.87 
TCGA-CW-5588 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5469 
       66.31         6.77        61.41        90.54        10.22        31.10 
TCGA-EU-5907 TCGA-G6-A8L8 TCGA-T7-A92I 
        4.18        35.87        11.70 

$`1P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 
       74.63        74.76        24.16        55.76        20.71        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        49.28        94.29        83.21 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
       28.47        19.00        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77         6.02        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        10.52        10.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 
        8.05         2.24        21.86        15.95        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       56.98       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       71.41       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
       89.49        91.46       126.05        35.90        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        31.66        24.82        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
       12.00         5.75         5.10         0.85         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        25.55        25.91        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        61.78        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       15.16         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
       10.82         5.33        61.97        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        31.30        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       18.51        38.70        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       28.87        48.10         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       19.82        44.55        34.95         0.95       115.00        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 
       63.25        73.22        14.17       106.16        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 
       10.72        74.27        75.06       116.84        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       63.98       115.69        26.93        50.01        24.66        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        49.97        51.25       108.56        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       85.78        73.18        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        79.63        91.69        55.33        94.45        10.85 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC 
       12.00        81.21        18.12         3.91         6.77         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       10.29        70.13         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC 
       16.37 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.53              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           117.80            149.16 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            40.01             38.43 
[1] "0.5 - 117.8 (40.0)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED        31        8         9        9
  1P LOSS WILD-TYPE     232       49       116       74
D42V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                31               232
  STAGE II                8                49
  STAGE III               9               116
  STAGE IV                9                74
[1] 4 2
[1] TRUE
[1] "dimension of 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    32   9  12   4
  1P LOSS WILD-TYPE 236  60 168   7
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              32               236
  T2               9                60
  T3              12               168
  T4               4                 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"
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    26   1
  1P LOSS WILD-TYPE 208  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     26    1
  1P LOSS WILD-TYPE  208   16
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              26               208
  1               1                16
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    49   6
  1P LOSS WILD-TYPE 369  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     49    6
  1P LOSS WILD-TYPE  369   72
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              49               369
  1               6                72
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    17  40
  1P LOSS WILD-TYPE 172 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     17   40
  1P LOSS WILD-TYPE  172  299
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              17               172
  MALE                40               299
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                20 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4VX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DV-A4W0        TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D42V10, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                11 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5550        TCGA-DV-A4W0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-MM-A563        TCGA-MM-A84U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         8    47
  1P LOSS WILD-TYPE     7                        48   410
D42V11, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               8                48
  WHITE                                  47               410
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     5  39
  1P LOSS WILD-TYPE  21 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   39
  1P LOSS WILD-TYPE   21  311
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              39               311
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    23  13
  1Q LOSS WILD-TYPE 328 162
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               36               490 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               162 
$`1Q LOSS MUTATED`
TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3465 
       43.20        18.64       117.80       112.08        94.19        12.13 
TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4821 TCGA-B0-4822 
       40.70        28.47         1.38         3.62        40.44        36.53 
TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5102 TCGA-B0-5117 TCGA-B2-3923 
       68.71        65.29        36.85        90.87        52.87        32.61 
TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4334 TCGA-BP-4353 TCGA-BP-4768 
        5.46        17.19         6.38        21.21        12.33        13.15 
TCGA-BP-4775 TCGA-BP-4968 TCGA-BP-4986 TCGA-BP-4994 TCGA-CJ-4897 TCGA-CJ-4901 
       60.59        57.40        25.81        43.00       109.84        47.67 
TCGA-CJ-4907 TCGA-CW-5588 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5469 
       49.28        66.31         6.77        61.41        90.54        31.10 

$`1Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91        29.10        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61       109.51        46.78        48.36        78.64        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       38.40        82.45        72.89         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 
        4.57         2.53         3.48        19.00        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 
       52.21        45.07        33.50        16.77         6.02        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07        29.03         2.27        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       15.95        62.89        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        66.05        38.63        52.73        41.88        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46       126.05        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        31.66        24.82        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         0.85         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       80.68        37.25        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       31.30        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.74        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61       105.37        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.25       108.56        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       79.63        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.00        81.21        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.38              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           117.80            149.16 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           40.570            38.415 
[1] "1.4 - 117.8 (40.6)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.1"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED        19        5         7        5
  1Q LOSS WILD-TYPE     244       52       118       78
D43V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                19               244
  STAGE II                5                52
  STAGE III               7               118
  STAGE IV                5                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED    19   5   9   3
  1Q LOSS WILD-TYPE 249  64 171   8
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              19               249
  T2               5                64
  T3               9               171
  T4               3                 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"
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    17   1
  1Q LOSS WILD-TYPE 217  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     17    1
  1Q LOSS WILD-TYPE  217   16
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              17               217
  1               1                16
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    33   3
  1Q LOSS WILD-TYPE 385  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     33    3
  1Q LOSS WILD-TYPE  385   75
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              33               385
  1               3                75
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11  25
  1Q LOSS WILD-TYPE 178 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   25
  1Q LOSS WILD-TYPE  178  314
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               178
  MALE                25               314
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
D43V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       1                         2    32
  1Q LOSS WILD-TYPE     7                        54   425
D43V11, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                54
  WHITE                                  32               425
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  27
  1Q LOSS WILD-TYPE  23 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   27
  1Q LOSS WILD-TYPE   23  323
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                23
  NOT HISPANIC OR LATINO              27               323
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    10   4
  2P LOSS WILD-TYPE 341 171
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               512 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4               171 
$`2P LOSS MUTATED`
TCGA-A3-3313 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 
       24.16        43.20       112.08        94.19        40.01        12.13 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4821 TCGA-B0-5117 TCGA-B2-3923 TCGA-BP-4334 
       40.70         3.62        40.44        52.87        32.61        21.21 
TCGA-BP-4994 TCGA-BP-5175 
       43.00        30.64 

$`2P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       38.40        82.45        72.89         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
      111.52       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46       126.05        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        31.66        24.82        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        1.74        74.20        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             3.62              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           112.08            149.16 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           40.225            38.415 
[1] "3.6 - 112.1 (40.2)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         8        3         2        1
  2P LOSS WILD-TYPE     255       54       123       82
D44V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 8               255
  STAGE II                3                54
  STAGE III               2               123
  STAGE IV                1                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     8   3   2   1
  2P LOSS WILD-TYPE 260  66 178  10
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               8               260
  T2               3                66
  T3               2               178
  T4               1                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"
D44V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     6   0
  2P LOSS WILD-TYPE 228  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    0
  2P LOSS WILD-TYPE  228   17
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               6               228
  1               0                17
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    13   1
  2P LOSS WILD-TYPE 405  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     13    1
  2P LOSS WILD-TYPE  405   77
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              13               405
  1               1                77
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     4  10
  2P LOSS WILD-TYPE 185 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4   10
  2P LOSS WILD-TYPE  185  329
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4               185
  MALE                10               329
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
D44V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       1                         3    10
  2P LOSS WILD-TYPE     7                        53   447
D44V11, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                53
  WHITE                                  10               447
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  10
  2P LOSS WILD-TYPE  26 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   10
  2P LOSS WILD-TYPE   26  340
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              10               340
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    10   4
  2Q LOSS WILD-TYPE 341 171
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               512 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4               171 
$`2Q LOSS MUTATED`
TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 
       43.20       112.08        94.19        40.01        12.13        40.70 
TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4821 TCGA-B0-5117 TCGA-B2-3923 TCGA-BP-4334 
       28.47         3.62        40.44        52.87        32.61        21.21 
TCGA-BP-4994 TCGA-BP-5175 
       43.00        30.64 

$`2Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68        68.61       109.51        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       78.64        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        82.45        72.89         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         2.53         3.48        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
      111.52       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46       126.05        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        31.66        24.82        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        1.74        74.20        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             3.62              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           112.08            149.16 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           40.225            38.415 
[1] "3.6 - 112.1 (40.2)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         7        3         3        1
  2Q LOSS WILD-TYPE     256       54       122       82
D45V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 7               256
  STAGE II                3                54
  STAGE III               3               122
  STAGE IV                1                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     7   3   3   1
  2Q LOSS WILD-TYPE 261  66 177  10
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               7               261
  T2               3                66
  T3               3               177
  T4               1                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"
D45V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     6   0
  2Q LOSS WILD-TYPE 228  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6    0
  2Q LOSS WILD-TYPE  228   17
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               6               228
  1               0                17
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    13   1
  2Q LOSS WILD-TYPE 405  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     13    1
  2Q LOSS WILD-TYPE  405   77
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              13               405
  1               1                77
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     4  10
  2Q LOSS WILD-TYPE 185 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4   10
  2Q LOSS WILD-TYPE  185  329
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               4               185
  MALE                10               329
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
D45V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       1                         2    11
  2Q LOSS WILD-TYPE     7                        54   446
D45V11, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                54
  WHITE                                  11               446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  11
  2Q LOSS WILD-TYPE  26 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   11
  2Q LOSS WILD-TYPE   26  339
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              11               339
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   253 126
  3P LOSS WILD-TYPE  98  49
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              379               147 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              126                49 
$`3P LOSS MUTATED`
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       12.66        36.82        47.21        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 
       38.47        48.82        62.01        34.29         4.50        52.93 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3365 
       29.92        18.44        88.37        42.97        82.32        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.64        18.87        28.31        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       29.10       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
      109.51        78.64        49.28        94.29        28.73        22.45 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 
       38.40        82.45        72.89         1.41         1.41         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
        3.48        28.47         5.98         2.14        19.73        57.70 
TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 
        6.64        15.72        46.59         0.59        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       27.42         6.71        56.68        10.52        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       43.30        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5108 
       21.86        52.08        15.95        90.87        90.48        58.59 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       66.05        38.63        52.73        41.88        51.02        38.43 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       46.39        42.41       111.52       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       71.41        73.84       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5639 
       89.49        91.46        35.90        31.96        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 
       21.57        16.67        12.00         5.10         0.85         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.55        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54F 
        0.85         6.38         0.53        34.39        14.30        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
        1.74         8.42         4.93        17.36        16.27       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4167 
       85.51        94.72        93.34        32.61         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4327 
       23.05        77.03        61.78        64.27        97.45         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68        37.25        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       31.89        12.33        72.59         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       48.07        13.15         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       68.38        11.64        48.95        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       60.30        61.22        61.51        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.90        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       31.30        25.81        36.95         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 
        5.82        45.07        30.64        41.62        18.51        37.02 
TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       27.62        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
        1.74        74.20        52.27        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        37.22        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 
       33.24        13.41        24.62        33.47        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 
       83.97        49.25        79.66        74.27        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       71.87        66.21        61.91        64.18        30.64        51.52 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5672 
       49.28        50.33        45.14         3.06       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 
      129.40       133.71        25.71        18.87        22.32       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        53.26       118.85        53.42        75.58 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 
      119.64         7.36        64.57        81.83         5.39        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66        63.39        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       79.53        18.44        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
        1.94        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5573 
       22.78        62.63        13.28        45.96        12.16        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-EU-5906 TCGA-EU-5907 
       66.28        56.84        53.46        81.21         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       10.29        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC 
       16.37 

$`3P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3362 
       11.90         0.53        37.38        31.07        45.53        51.25 
TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3440 
       10.49        43.20        65.52       117.80        73.08        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
       46.78        48.36        40.01        83.21        37.58        12.13 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
       40.70         3.32         4.57        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4814 
       65.10         7.82        43.96         3.25        58.45         5.52 
TCGA-B0-4834 TCGA-B0-4839 TCGA-B0-4844 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       68.71        53.88        10.29        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5117 
       25.32        62.89        52.54        30.48        19.30        52.87 
TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5705 TCGA-B0-5812 TCGA-B2-3923 
       48.82        56.98       112.80       149.16       126.05        32.61 
TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5835 
        1.68        21.30        31.30        24.82         5.75         0.53 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5165 
       42.71        25.05        45.37        17.19        25.91        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54K 
       50.14        16.60        48.53        27.29        29.88        15.42 
TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4173 TCGA-BP-4177 
       14.17        90.28       101.06        99.85        62.24        54.90 
TCGA-BP-4326 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4349 TCGA-BP-4352 
       53.42        21.21        15.16         0.07        12.23        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       33.99        31.33        12.30        77.98        77.62        44.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4790 
       61.68        10.82        60.59        60.95        15.78        36.53 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       20.38        37.25        47.97         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 
       14.24        53.65        27.22        43.00        38.70        37.48 
TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5186 TCGA-BP-5191 TCGA-BP-5192 
       79.30        30.64         9.63        22.78        31.79        23.47 
TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4884 
       19.82        14.17       106.16        10.72       116.84        57.83 
TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4912 TCGA-CJ-4913 
      113.46        63.98       115.69       109.84        54.48        38.56 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6031 
        4.57        18.81        25.25        18.15        67.00        62.66 
TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-6087 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4862 
       92.02        85.78         1.35       103.43        46.16       107.54 
TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       61.41        23.74        79.63         2.40        31.10        12.69 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       65.88        11.67        23.90        12.00        18.12         3.91 
TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-T7-A92I 
        7.96        70.13        11.70 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.10              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           133.94            149.16 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            39.45             33.99 
[1] "0.1 - 133.9 (39.5)" "0.1 - 149.2 (34.0)"
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED       184       42       101       53
  3P LOSS WILD-TYPE      79       15        24       30
D46V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I               184                79
  STAGE II               42                15
  STAGE III             101                24
  STAGE IV               53                30
[1] 4 2
[1] TRUE
[1] "dimension of 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   187  51 138   4
  3P LOSS WILD-TYPE  81  18  42   7
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1             187                81
  T2              51                18
  T3             138                42
  T4               4                 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"
D46V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   165  11
  3P LOSS WILD-TYPE  69   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    165   11
  3P LOSS WILD-TYPE   69    6
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             165                69
  1              11                 6
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   307  50
  3P LOSS WILD-TYPE 111  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    307   50
  3P LOSS WILD-TYPE  111   28
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             307               111
  1              50                28
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   123 257
  3P LOSS WILD-TYPE  66  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    123  257
  3P LOSS WILD-TYPE   66   82
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             123                66
  MALE               257                82
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       5                        35   334
  3P LOSS WILD-TYPE     3                        21   123
D46V11, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   5                 3
  BLACK OR AFRICAN AMERICAN              35                21
  WHITE                                 334               123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    20 248
  3P LOSS WILD-TYPE   6 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     20  248
  3P LOSS WILD-TYPE    6  102
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                  20                 6
  NOT HISPANIC OR LATINO             248               102
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    67  32
  3Q LOSS WILD-TYPE 284 143
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               99               427 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               32               143 
$`3Q LOSS MUTATED`
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3346 TCGA-A3-3347 
       24.16        49.02        48.59        38.99         4.50        52.93 
TCGA-A3-3357 TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3387 
       88.37        28.70        24.16        18.64        18.87        20.28 
TCGA-A3-A6NI TCGA-A3-A6NN TCGA-AK-3425 TCGA-AK-3433 TCGA-AK-3460 TCGA-B0-4693 
       33.47         0.10       109.91       112.08        82.45         2.53 
TCGA-B0-4696 TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4822 TCGA-B0-4823 
       28.47        46.59        52.21        33.50        36.53        14.93 
TCGA-B0-4836 TCGA-B0-4845 TCGA-B0-5094 TCGA-B0-5099 TCGA-B0-5115 TCGA-B0-5120 
       40.70        65.29        10.95        15.95        52.73        38.43 
TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-5639 TCGA-B8-4148 TCGA-B8-5163 TCGA-B8-A54I 
       89.49        35.90        32.98        27.16        27.02         4.93 
TCGA-BP-4158 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4347 
      111.02         0.43        23.05        74.17        54.77        44.94 
TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4777 TCGA-BP-4781 
       31.89        12.33        41.75        13.15        56.91        68.38 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4963 TCGA-BP-4977 TCGA-BP-4986 
       36.39        36.95         6.71        60.30        14.93        25.81 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5008 TCGA-BP-5173 TCGA-BP-5180 
       16.47        30.64        41.62        35.21         1.74        74.40 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
       37.22        13.35        27.02        24.62        44.55        34.95 
TCGA-CJ-4635 TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4882 
       46.55       105.37        11.05        74.27        75.06        61.91 
TCGA-CJ-4888 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5689 
       51.52       108.56        49.28        22.32       122.83        53.26 
TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
      118.85        83.90        14.66        63.39        93.04        63.42 
TCGA-CZ-5452 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       58.82        90.54        55.33        10.85        10.22        21.76 
TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-DV-5573 TCGA-DV-5574 
        1.94        67.96        12.26        14.63        37.15        66.28 
TCGA-EU-5907 TCGA-GK-A6C7 TCGA-MM-A564 
        4.18         2.01        19.96 

$`3Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3325 TCGA-A3-3326 
       49.08        37.15        49.58        36.36        38.47        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01        34.29        31.07        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 
       18.44        42.97        82.32        51.25        10.49        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        20.71        28.31 
TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       65.52        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61       109.51        94.19        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       37.58        38.40        72.89        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        3.32         1.41         4.57         3.48        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
        0.59         5.52        45.07        16.77         6.02        40.44 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        68.71        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       18.51        15.09         8.05         2.24        21.86        52.08 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       19.30        66.05        38.63        41.88        52.87        51.02 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
      105.37       130.65        79.89       131.15        91.46       126.05 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       32.61         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       24.82        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       23.31        16.80        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        1.74         8.42        17.36        15.42        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       99.85        89.36        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       80.68        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4352 
       18.48        52.24        62.86        49.08        12.23        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        44.15        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 
        5.33        61.97        60.59        13.51        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        31.30        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 
        3.88        46.45         5.82        43.00        45.07        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5009 TCGA-BP-5010 
       38.70        37.02        27.62        37.48        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10         6.35        79.30        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        62.86        49.15        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 
       22.78        33.24        31.79        23.47        13.41        33.47 
TCGA-BP-5198 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       19.82        31.27         0.95       115.00        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 
       14.17       106.16       114.41        54.61        58.95        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4876 
       83.97        49.25        79.66        10.72       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        66.21        57.83       113.46        64.18        30.64 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       51.25        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
      133.71        25.71        18.87        25.25        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       73.35        67.00        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-4866 
       69.21        58.75         6.77       107.54         5.46        61.41 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5460 
       79.53        23.74        18.44        79.63        91.69        94.45 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       69.96        84.30        22.52         2.40        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       80.19        65.65        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       65.88        12.16        11.67        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC 
       12.00        81.21        18.12         3.91         6.77         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
       10.29        70.13        35.87        19.43        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.10              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           122.83            149.16 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            36.53             39.16 
[1] "0.1 - 122.8 (36.5)" "0.1 - 149.2 (39.2)"
[1] "hr=" "1"  
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED        48       15        22       14
  3Q LOSS WILD-TYPE     215       42       103       69
D47V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                48               215
  STAGE II               15                42
  STAGE III              22               103
  STAGE IV               14                69
[1] 4 2
[1] TRUE
[1] "dimension of 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    51  17  31   0
  3Q LOSS WILD-TYPE 217  52 149  11
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              51               217
  T2              17                52
  T3              31               149
  T4               0                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"
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    38   1
  3Q LOSS WILD-TYPE 196  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     38    1
  3Q LOSS WILD-TYPE  196   16
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              38               196
  1               1                16
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    80  14
  3Q LOSS WILD-TYPE 338  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     80   14
  3Q LOSS WILD-TYPE  338   64
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              80               338
  1              14                64
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    19  80
  3Q LOSS WILD-TYPE 170 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     19   80
  3Q LOSS WILD-TYPE  170  259
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              19               170
  MALE                80               259
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         8    88
  3Q LOSS WILD-TYPE     7                        48   369
D47V11, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               8                48
  WHITE                                  88               369
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  57
  3Q LOSS WILD-TYPE  21 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   57
  3Q LOSS WILD-TYPE   21  293
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              57               293
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    33  39
  4P LOSS WILD-TYPE 318 136
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72               454 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               39               136 
$`4P LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3352 TCGA-A3-3373 TCGA-A3-3380 TCGA-A3-3385 TCGA-AK-3436 
       49.08        18.44        53.29        18.64        65.52       109.51 
TCGA-AK-3458 TCGA-B0-4690 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4811 
       38.40         1.41        19.73        57.70        43.96        46.59 
TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-4845 
        5.52        40.44        36.53        10.09        10.29        65.29 
TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5113 TCGA-B0-5116 
       36.85         7.30         8.05        52.08        38.63        41.88 
TCGA-B0-5399 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4154 TCGA-B8-5158 
       46.39         0.53         5.46        23.31        45.37        20.91 
TCGA-B8-5162 TCGA-B8-5549 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4343 TCGA-BP-4351 
        1.18         6.38        90.28        32.61        62.86        31.89 
TCGA-BP-4353 TCGA-BP-4762 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4974 
       12.33        44.15        13.15        10.82        15.78         6.90 
TCGA-BP-5173 TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4644 TCGA-CJ-4878 
        1.74        42.44        33.47        19.82        11.05        71.87 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4913 TCGA-CJ-5676 
       27.65       109.84        51.25        49.28        38.56       133.71 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CW-5580 TCGA-CW-5588 
       25.71        22.32        53.42        75.58        64.57        66.31 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 
       83.90        18.77        47.08        69.21         6.77        61.41 
TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-EU-5907 TCGA-G6-A8L7 
       90.54        10.85        84.30        31.10         4.18        70.13 

$`4P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       31.07         4.50        52.93        45.53        29.92        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 
       74.76        24.16        43.20        55.76        20.71        18.87 
TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       94.19        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 
       94.29        83.21        28.73        22.45        37.58        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         3.32         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        2.53         3.48        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 
       65.10         7.82         5.98         2.14         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         0.59        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       16.77         6.02        14.93        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       56.68        10.52        39.45        26.07        29.03         2.27 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       70.52        20.94        43.30        11.24        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       18.51        15.09        10.95         2.24        21.86        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       19.30        66.05        52.73        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       48.82        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         5.10         0.85         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 
       16.80        27.16        42.71        25.05        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       25.91        50.14        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       94.72       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        74.17        54.77        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.62         5.98        41.75        71.80        48.07        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        60.95        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        49.15        38.30        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        44.55        34.95        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61       105.37        58.95        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 
       39.45        50.24        56.35        47.67        49.97       108.56 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       49.18        50.33        54.48        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5680 
       18.81       131.08        72.00       129.40        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 
      118.85        62.66       119.64         7.36        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 
      105.93       103.43        25.45        46.16         0.59        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66       107.54        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       55.33        94.45        10.22        21.76        69.96        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        6.77         7.96        10.29        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.53              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           133.71            149.16 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           37.625            38.585 
[1] "0.5 - 133.7 (37.6)" "0.1 - 149.2 (38.6)"
[1] "hr=" "2.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED        21        6        25       20
  4P LOSS WILD-TYPE     242       51       100       63
D48V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                21               242
  STAGE II                6                51
  STAGE III              25               100
  STAGE IV               20                63
[1] 4 2
[1] TRUE
[1] "dimension of 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    22   8  38   4
  4P LOSS WILD-TYPE 246  61 142   7
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              22               246
  T2               8                61
  T3              38               142
  T4               4                 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"
D48V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    33   3
  4P LOSS WILD-TYPE 201  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     33    3
  4P LOSS WILD-TYPE  201   14
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              33               201
  1               3                14
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    53  18
  4P LOSS WILD-TYPE 365  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     53   18
  4P LOSS WILD-TYPE  365   60
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              53               365
  1              18                60
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    25  47
  4P LOSS WILD-TYPE 164 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25   47
  4P LOSS WILD-TYPE  164  292
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              25               164
  MALE                47               292
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                19 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E        TCGA-B8-A54F 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4VX        TCGA-DV-A4W0 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-MM-A563        TCGA-T7-A92I 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D48V10, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                10 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5550        TCGA-DV-A4W0        TCGA-MM-A563 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-MM-A84U        TCGA-T7-A92I 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       1                         2    67
  4P LOSS WILD-TYPE     7                        54   390
D48V11, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                54
  WHITE                                  67               390
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5  49
  4P LOSS WILD-TYPE  21 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5   49
  4P LOSS WILD-TYPE   21  301
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              49               301
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    28  37
  4Q LOSS WILD-TYPE 323 138
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65               461 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               37               138 
$`4Q LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3373 TCGA-A3-3380 TCGA-AK-3436 
       49.08         4.50        18.44        53.29        18.64       109.51 
TCGA-AK-3458 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       38.40         3.32         1.41        19.73        57.70        43.96 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4844 
       46.59         5.52        40.44        36.53        10.09        10.29 
TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5113 
       65.29        36.85         7.30         8.05        52.08        38.63 
TCGA-B0-5116 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5549 
       41.88         5.46        23.31        20.91         1.18         6.38 
TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4768 
       90.28        32.61        62.86        31.89        12.33        13.15 
TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4974 TCGA-BP-5173 TCGA-BP-5183 TCGA-BP-5196 
       10.82        15.78         6.90         1.74        42.44        33.47 
TCGA-BP-5198 TCGA-CJ-4644 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 
       19.82        11.05        66.21       109.84        51.25        49.28 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5580 TCGA-CW-5588 
      133.71        25.71        22.32        53.42        64.57        66.31 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 
       83.90        18.77        47.08        69.21         6.77        61.41 
TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-EU-5907 
       90.54        10.85        84.30        31.10         4.18 

$`4Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 
       31.07        52.93        45.53        29.92        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 
       24.16        43.20        55.76        20.71        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       94.19        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 
       94.29        83.21        28.73        22.45        37.58        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        7.82         5.98         2.14         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       15.72         0.59        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 
        6.02        14.93        54.48        29.10        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       10.52        39.45        26.07        29.03         2.27        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       15.09        10.95         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       66.05        52.73        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        5.75         5.10         0.85         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        25.91        50.14        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 
        0.85        24.23        50.14        16.60        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
      111.02        85.51        94.72       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        74.17        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       71.80        48.07        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
       13.51        56.91        68.38        11.64        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
       58.98        14.24        48.89        49.38        45.50        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       28.87        48.10         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
       31.79        23.47        13.41        24.62        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06       116.84        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       56.35        47.67        49.97       108.56        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
      131.08        72.00       129.40        18.87        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66       119.64         7.36        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 
      105.93       103.43        25.45        46.16         0.59        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66       107.54        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       55.33        94.45        10.22        21.76        69.96        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        6.77         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             1.18              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           133.71            149.16 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            32.61             39.16 
[1] "1.2 - 133.7 (32.6)" "0.1 - 149.2 (39.2)"
[1] "hr=" "2.3"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED        15        6        23       21
  4Q LOSS WILD-TYPE     248       51       102       62
D49V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                15               248
  STAGE II                6                51
  STAGE III              23               102
  STAGE IV               21                62
[1] 4 2
[1] TRUE
[1] "dimension of 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    16   8  36   5
  4Q LOSS WILD-TYPE 252  61 144   6
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              16               252
  T2               8                61
  T3              36               144
  T4               5                 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"
D49V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    27   3
  4Q LOSS WILD-TYPE 207  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     27    3
  4Q LOSS WILD-TYPE  207   14
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              27               207
  1               3                14
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    46  19
  4Q LOSS WILD-TYPE 372  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     46   19
  4Q LOSS WILD-TYPE  372   59
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              46               372
  1              19                59
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    19  46
  4Q LOSS WILD-TYPE 170 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     19   46
  4Q LOSS WILD-TYPE  170  293
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              19               170
  MALE                46               293
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                20 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E        TCGA-B8-A54F 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4VX        TCGA-DV-A4W0 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563        TCGA-T7-A92I 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
D49V10, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                11 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5550        TCGA-DV-A4W0        TCGA-G6-A8L7 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-MM-A563        TCGA-MM-A84U        TCGA-T7-A92I 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       1                         1    61
  4Q LOSS WILD-TYPE     7                        55   396
D49V11, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               1                55
  WHITE                                  61               396
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4  43
  4Q LOSS WILD-TYPE  22 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4   43
  4Q LOSS WILD-TYPE   22  307
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              43               307
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     2   5
  5P LOSS WILD-TYPE 349 170
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               519 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5               170 
$`5P LOSS MUTATED`
TCGA-AK-3433 TCGA-B0-4688 TCGA-B0-5107 TCGA-B8-4143 TCGA-BP-4770 TCGA-CJ-4901 
      112.08         3.32        30.48        23.31        10.82        47.67 
TCGA-CZ-5469 
       31.10 

$`5P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        2.53         3.48        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         6.90        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.74        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95       115.00        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      105.37        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45       109.84        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
      107.54        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       69.96        84.30        22.52         2.40         1.94        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.32              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           112.08            149.16 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            30.48             38.56 
[1] "3.3 - 112.1 (30.5)" "0.1 - 149.2 (38.6)"
[1] "hr=" "2.7"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0        2         1        4
  5P LOSS WILD-TYPE     263       55       124       79
D50V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0               263
  STAGE II                2                55
  STAGE III               1               124
  STAGE IV                4                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED     0   3   2   2
  5P LOSS WILD-TYPE 268  66 178   9
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0               268
  T2               3                66
  T3               2               178
  T4               2                 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"
D50V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     6   0
  5P LOSS WILD-TYPE 228  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    0
  5P LOSS WILD-TYPE  228   17
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6               228
  1               0                17
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4   3
  5P LOSS WILD-TYPE 414  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    3
  5P LOSS WILD-TYPE  414   75
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               4               414
  1               3                75
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4   3
  5P LOSS WILD-TYPE 185 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    3
  5P LOSS WILD-TYPE  185  336
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               4               185
  MALE                 3               336
[1] 2 2
[1] FALSE
D50V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                51 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4622        TCGA-B8-5158        TCGA-CJ-6028 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5982        TCGA-DV-5565 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DV-A4VX        TCGA-DV-A4VZ        TCGA-DV-A4W0        TCGA-EU-5904 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907        TCGA-G6-A8L6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D50V9, continuous
D50V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     7
  5P LOSS WILD-TYPE     8                        56   450
D50V11, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               0                56
  WHITE                                   7               450
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0   6
  5P LOSS WILD-TYPE  26 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    6
  5P LOSS WILD-TYPE   26  344
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               6               344
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     2   4
  5Q LOSS WILD-TYPE 349 171
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               520 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4               171 
$`5Q LOSS MUTATED`
TCGA-AK-3433 TCGA-B0-4688 TCGA-B8-4143 TCGA-BP-4770 TCGA-CJ-4901 TCGA-CZ-5469 
      112.08         3.32        23.31        10.82        47.67        31.10 

$`5Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        2.53         3.48        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       80.68        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       44.94        12.23        31.89        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.74        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61       105.37        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        49.97        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66       107.54        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.00        81.21        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             3.32              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           112.08            149.16 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           27.205            38.515 
[1] "3.3 - 112.1 (27.2)" "0.1 - 149.2 (38.5)"
[1] "hr=" "2.5"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         0        2         1        3
  5Q LOSS WILD-TYPE     263       55       124       80
D51V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0               263
  STAGE II                2                55
  STAGE III               1               124
  STAGE IV                3                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"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED     0   2   2   2
  5Q LOSS WILD-TYPE 268  67 178   9
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0               268
  T2               2                67
  T3               2               178
  T4               2                 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"
D51V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5   0
  5Q LOSS WILD-TYPE 229  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    0
  5Q LOSS WILD-TYPE  229   17
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               5               229
  1               0                17
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     4   2
  5Q LOSS WILD-TYPE 414  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4    2
  5Q LOSS WILD-TYPE  414   76
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               4               414
  1               2                76
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     3   3
  5Q LOSS WILD-TYPE 186 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    3
  5Q LOSS WILD-TYPE  186  336
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3               186
  MALE                 3               336
[1] 2 2
[1] FALSE
D51V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                51 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4622        TCGA-B8-5158        TCGA-CJ-6028 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5982        TCGA-DV-5565 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DV-A4VX        TCGA-DV-A4VZ        TCGA-DV-A4W0        TCGA-EU-5904 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907        TCGA-G6-A8L6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D51V9, continuous
D51V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         0     6
  5Q LOSS WILD-TYPE     8                        56   451
D51V11, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               0                56
  WHITE                                   6               451
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0   5
  5Q LOSS WILD-TYPE  26 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    5
  5Q LOSS WILD-TYPE   26  345
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               5               345
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    64  36
  6P LOSS WILD-TYPE 287 139
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              100               426 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               36               139 
$`6P LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 
       36.82        49.08        37.15        62.01        34.29         4.50 
TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 TCGA-AK-3426 
       52.93        18.44        43.20        18.64        18.87        29.10 
TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 
       15.78       112.08        68.61       109.51        94.19        40.01 
TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 
       38.40        12.13        40.70         1.41         3.48        28.47 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4813 TCGA-B0-4822 
        1.38         3.62        19.73        43.96         0.59        36.53 
TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-5084 TCGA-B0-5108 
       54.48        10.09        40.70        10.29         7.30        58.59 
TCGA-B0-5117 TCGA-B0-5702 TCGA-B2-3923 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5838 
       52.87        71.41        32.61        12.00         5.10         5.46 
TCGA-B8-4620 TCGA-B8-5158 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4327 
       25.55        20.91        32.61        89.36        64.27         3.58 
TCGA-BP-4334 TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 TCGA-BP-4768 
       21.21        74.17        11.31        12.33         5.98        13.15 
TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 
       10.82        60.59        15.78        36.39        87.45        71.41 
TCGA-BP-4962 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4992 TCGA-BP-4994 
       58.68        57.40        46.45        25.81        16.47        43.00 
TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5191 
        6.35        30.64        62.86        74.40        37.22        31.79 
TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4881 TCGA-CJ-4887 
       31.27        46.55        79.66        10.72        66.21        30.64 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CJ-5679 
      109.84        47.67       108.56        49.28       133.71        22.32 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4866 
      118.85        53.42        66.31        25.45        69.21        61.41 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5987 
       58.82        79.63        84.30         1.94        67.96        14.63 
TCGA-DV-5568 TCGA-EU-5907 TCGA-G6-A8L7 TCGA-MM-A563 
       12.16         4.18        70.13        19.43 

$`6P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        47.21         0.53        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       49.02        49.58        48.59        36.36        38.99        38.47 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       37.38        48.82        31.07        45.53        29.92        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 
       74.76        24.16        53.29        55.76        20.71        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        0.10        11.18        10.62       109.91       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 
      109.41        73.68        46.78        48.36        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 
       94.29        83.21        28.73        22.45        37.58        82.45 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 
       72.89         1.41         3.32         4.57         2.53        19.00 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 
        3.25        58.45        15.72        46.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        40.44        14.93 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       29.10        78.44        68.71        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        10.52        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       38.63        52.73        41.88        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
      126.28        80.91        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       79.89       131.15        89.49        91.46       126.05        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       32.98        21.57        16.67         5.75         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.91        50.14 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       94.72        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        61.78        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 
       53.42        27.78        62.07        80.68        37.25        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        31.89        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98        77.62        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       71.80        48.07        61.68         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        60.95        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       20.38        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        6.94        63.62        60.30        61.22        61.51         6.74 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 
       47.11        53.65        14.93        36.07        33.34        31.30 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 
       36.95        27.22         3.88        46.45         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 
       37.48        35.21        36.23        28.87        48.10        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 
        1.74        74.20        52.27         9.63        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        61.91        57.83       113.46        64.18 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       27.65        39.45        50.24        56.35        49.97        51.25 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
        4.57        18.81       131.08        72.00       129.40        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       67.00        53.26        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77        46.16         0.59        47.08        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66       107.54        63.39        93.04         5.46        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        69.96        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
        2.40        31.10        12.69        80.19        65.65        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 
       22.78        62.63        13.28        45.96        65.88        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       81.21        18.12         3.91         6.77         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.96        23.01        16.37        11.70 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.59              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           133.71            149.16 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           36.675            38.845 
[1] "0.6 - 133.7 (36.7)" "0.1 - 149.2 (38.8)"
[1] "hr=" "1.2"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED        38       13        27       22
  6P LOSS WILD-TYPE     225       44        98       61
D52V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                38               225
  STAGE II               13                44
  STAGE III              27                98
  STAGE IV               22                61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED    38  15  43   4
  6P LOSS WILD-TYPE 230  54 137   7
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              38               230
  T2              15                54
  T3              43               137
  T4               4                 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"
D52V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    37   7
  6P LOSS WILD-TYPE 197  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     37    7
  6P LOSS WILD-TYPE  197   10
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              37               197
  1               7                10
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    79  19
  6P LOSS WILD-TYPE 339  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     79   19
  6P LOSS WILD-TYPE  339   59
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              79               339
  1              19                59
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    22  78
  6P LOSS WILD-TYPE 167 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     22   78
  6P LOSS WILD-TYPE  167  261
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              22               167
  MALE                78               261
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
D52V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         4    93
  6P LOSS WILD-TYPE     7                        52   364
D52V11, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               4                52
  WHITE                                  93               364
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  65
  6P LOSS WILD-TYPE  21 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   65
  6P LOSS WILD-TYPE   21  285
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              65               285
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    90  38
  6Q LOSS WILD-TYPE 261 137
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              128               398 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               38               137 
$`6Q LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3335 
       36.82        49.08        49.02        37.15        49.58        62.01 
TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 
       34.29         4.50        52.93        18.44        43.20        18.64 
TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 
       18.87         0.10        29.10        15.78       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 
      109.51        94.19        40.01        38.40        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 
        1.41         3.48        28.47         1.38         3.62        19.73 
TCGA-B0-4712 TCGA-B0-4810 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4836 
       43.96        15.72        36.53        54.48        10.09        40.70 
TCGA-B0-4844 TCGA-B0-4849 TCGA-B0-5084 TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5119 
       10.29         2.27         7.30        58.59        52.87        51.02 
TCGA-B0-5402 TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       42.41        71.41        32.61        21.57        12.00         5.10 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-A54G 
        0.53         5.46        27.16        25.55        20.91         1.74 
TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4334 
       32.61        89.36        64.27        97.45         3.58        21.21 
TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4770 
       74.17        11.31        12.33         5.98        13.15        10.82 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 
       60.59        56.91        15.78        36.39        87.45        71.41 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       58.68        60.30        57.40        46.45        25.81        36.95 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 
       16.47        43.00        18.51         6.35        30.64        62.86 
TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 
       74.40        37.22        31.79        31.27       115.00        46.55 
TCGA-CJ-4643 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4893 
       58.95        79.66        10.72        66.21        30.64        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5675 
       39.45       109.84        47.67       108.56        49.28       129.40 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5584 
      133.71        22.32       118.85        53.42       119.64         5.39 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4866 
       85.78        66.31        25.45        69.21        58.75        61.41 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5984 
       58.82        79.63        94.45        84.30        80.19        67.96 
TCGA-CZ-5987 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5907 TCGA-G6-A8L7 
       14.63        12.16        37.15        56.84         4.18        70.13 
TCGA-MM-A563 TCGA-MW-A4EC 
       19.43        16.37 

$`6Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        47.21         0.53        39.16        24.16 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        38.47        37.38        48.82 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       31.07        45.53        29.92        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       53.29        55.76        20.71        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW 
       33.47        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 
      109.91       117.80        73.08       109.41        73.68        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        78.64        49.28        94.29        83.21        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       22.45        37.58        82.45        72.89         1.41         3.32 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        4.57         2.53        19.00        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 
        2.14        57.70         6.64         3.25        58.45        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 
        6.02        40.44        14.93        29.10        78.44        68.71 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 
       65.29        39.45        26.07        29.03        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 
       19.30        66.05        38.63        52.73        41.88        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       48.82        46.39        56.98       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
      126.28        80.91        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       79.89       131.15        89.49        91.46       126.05        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
       32.98        16.67         5.75         0.85         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        23.31        16.80        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       17.19        25.91        50.14        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85         0.43        23.05        77.03        62.24        61.78 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       54.90        53.42        27.78        62.07        80.68        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       15.16         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       31.33        12.30        72.59        77.98        77.62        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        48.07        61.68         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       13.51        68.38        11.64        60.95        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       20.38        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 
        6.94        63.62        61.22        61.51         6.74        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4988 
       53.65        14.93        36.07        33.34        31.30        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        3.88        46.45         5.82        45.07        30.64        41.62 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       28.87        48.10        79.30         1.74        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
        9.63        49.15        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4636 
       33.47        19.82        44.55        34.95         0.95        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 
       11.05        21.24        83.97        49.25        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
      116.84        64.27        71.87        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       64.18        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       27.65        50.24        56.35        49.97        51.25        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
       18.81       131.08        72.00        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66         7.36        64.57        92.02        81.83 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4860 
      103.43        18.77        46.16         0.59        47.08         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66       107.54        63.39        93.04         5.46        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        69.96        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
        1.94        31.10        12.69        65.65        12.26        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 
       62.63        13.28        45.96        65.88        11.67        66.28 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 
        6.77         7.96        10.29        35.87         2.01        19.96 
TCGA-MM-A84U TCGA-T7-A92I 
       23.01        11.70 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.10              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           133.71            149.16 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           37.810            38.515 
[1] "0.1 - 133.7 (37.8)" "0.1 - 149.2 (38.5)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED        57       17        29       25
  6Q LOSS WILD-TYPE     206       40        96       58
D53V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                57               206
  STAGE II               17                40
  STAGE III              29                96
  STAGE IV               25                58
[1] 4 2
[1] TRUE
[1] "dimension of 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    57  19  47   5
  6Q LOSS WILD-TYPE 211  50 133   6
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              57               211
  T2              19                50
  T3              47               133
  T4               5                 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"
D53V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    46   9
  6Q LOSS WILD-TYPE 188   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     46    9
  6Q LOSS WILD-TYPE  188    8
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              46               188
  1               9                 8
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   102  21
  6Q LOSS WILD-TYPE 316  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    102   21
  6Q LOSS WILD-TYPE  316   57
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             102               316
  1              21                57
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    37  91
  6Q LOSS WILD-TYPE 152 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     37   91
  6Q LOSS WILD-TYPE  152  248
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              37               152
  MALE                91               248
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
D53V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       2                         7   116
  6Q LOSS WILD-TYPE     6                        49   341
D53V11, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   2                 6
  BLACK OR AFRICAN AMERICAN               7                49
  WHITE                                 116               341
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     8  83
  6Q LOSS WILD-TYPE  18 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      8   83
  6Q LOSS WILD-TYPE   18  267
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                18
  NOT HISPANIC OR LATINO              83               267
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     1   2
  7P LOSS WILD-TYPE 350 173
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               523 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               173 
$`7P LOSS MUTATED`
TCGA-B0-4698 TCGA-BP-4761 TCGA-DV-A4VX 
        1.38         5.98        53.46 

$`7P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       94.19        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.62        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       66.28        56.84        23.90        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1.38              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            53.46            149.16 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             5.98             38.47 
[1] "1.4 - 53.5 (6.0)"   "0.1 - 149.2 (38.5)"
[1] "hr=" "4.1"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED         0        0         1        2
  7P LOSS WILD-TYPE     263       57       124       81
D54V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 0               263
  STAGE II                0                57
  STAGE III               1               124
  STAGE IV                2                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED     0   0   2   1
  7P LOSS WILD-TYPE 268  69 178  10
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               0               268
  T2               0                69
  T3               2               178
  T4               1                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"
D54V5, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1   1
  7P LOSS WILD-TYPE 233  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    1
  7P LOSS WILD-TYPE  233   16
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               1               233
  1               1                16
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   0
  7P LOSS WILD-TYPE 416  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    0
  7P LOSS WILD-TYPE  416   78
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               2               416
  1               0                78
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   3
  7P LOSS WILD-TYPE 189 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE  189  336
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               0               189
  MALE                 3               336
[1] 2 2
[1] FALSE
D54V8, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                52 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-DV-A4VZ        TCGA-DV-A4W0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G6-A8L6        TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
D54V9, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                20 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4W0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563        TCGA-T7-A92I 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
D54V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       0                         1     2
  7P LOSS WILD-TYPE     8                        55   455
D54V11, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                55
  WHITE                                   2               455
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   2
  7P LOSS WILD-TYPE  26 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE   26  348
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               2               348
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     2   2
  7Q LOSS WILD-TYPE 349 173
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               522 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               173 
$`7Q LOSS MUTATED`
TCGA-B0-4698 TCGA-BP-4761 TCGA-CJ-4912 TCGA-DV-A4VX 
        1.38         5.98        54.48        53.46 

$`7Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       94.19        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.62        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 
      108.56        49.18        49.28        50.33        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       56.84        23.90        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.38              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            54.48            149.16 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            29.72             38.45 
[1] "1.4 - 54.5 (29.7)"  "0.1 - 149.2 (38.5)"
[1] "hr=" "2.2"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         0        1         1        2
  7Q LOSS WILD-TYPE     263       56       124       81
D55V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 0               263
  STAGE II                1                56
  STAGE III               1               124
  STAGE IV                2                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED     0   1   2   1
  7Q LOSS WILD-TYPE 268  68 178  10
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0               268
  T2               1                68
  T3               2               178
  T4               1                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"
D55V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   1
  7Q LOSS WILD-TYPE 233  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    1
  7Q LOSS WILD-TYPE  233   16
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               1               233
  1               1                16
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   0
  7Q LOSS WILD-TYPE 415  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    0
  7Q LOSS WILD-TYPE  415   78
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               3               415
  1               0                78
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   4
  7Q LOSS WILD-TYPE 189 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    4
  7Q LOSS WILD-TYPE  189  335
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               0               189
  MALE                 4               335
[1] 2 2
[1] FALSE
D55V8, continuous
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                52 
       TCGA-3Z-A93Z        TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-DV-A4VZ        TCGA-DV-A4W0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G6-A8L6        TCGA-G6-A8L7        TCGA-G6-A8L8        TCGA-T7-A92I 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D55V9, continuous
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                20 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4W0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563        TCGA-T7-A92I 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D55V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         1     3
  7Q LOSS WILD-TYPE     8                        55   454
D55V11, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                55
  WHITE                                   3               454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   2
  7Q LOSS WILD-TYPE  25 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE   25  348
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO               2               348
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    84  53
  8P LOSS WILD-TYPE 267 122
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              137               389 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               53               122 
$`8P LOSS MUTATED`
TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3365 TCGA-A3-3372 
       37.15        38.47        34.29         4.50        28.70        24.16 
TCGA-A3-3373 TCGA-A3-3382 TCGA-A3-A6NN TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3434 
       53.29        18.87         0.10       109.91        29.10        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3458 TCGA-AS-3777 TCGA-B0-4688 
      109.51        94.19        40.01        38.40        40.70         3.32 
TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4718 
       28.47         3.62         5.98        19.73        43.96        58.45 
TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        0.59        52.21        45.07         6.02        40.44        36.53 
TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4845 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5094 
       40.70        27.42        65.29         2.27        70.52        10.95 
TCGA-B0-5102 TCGA-B0-5108 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5712 TCGA-B0-5713 
       90.87        58.59        70.68        85.78        89.49        91.46 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4151 
       16.67        12.00         5.46        23.31        27.16        42.71 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5551 
       20.91        27.02         0.85        50.14         6.38         0.53 
TCGA-B8-A54I TCGA-BP-4164 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4327 
        4.93        32.61        61.78        64.27        53.42         3.58 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4351 
       93.99        18.48        52.24        62.86        44.94        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       11.31        12.33        60.59        68.38        11.64        15.78 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4965 
       10.98        37.25         6.94        87.45        71.41        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4986 TCGA-BP-4994 
        6.74        57.40        14.24        45.50        25.81        43.00 
TCGA-BP-4998 TCGA-BP-5004 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5182 
       30.64        37.02         1.74        30.64         9.63        38.30 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
       34.95        31.27       114.41       105.37        58.95        21.24 
TCGA-CJ-4870 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 
       49.25        64.27        71.87        66.21        57.83       113.46 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 
       51.52        63.98        27.65       109.84        51.25       108.56 
TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5689 
       49.28        54.48        72.00        25.71        22.32        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6033 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4854 
      118.85        75.58         7.36       105.93        83.90        46.16 
TCGA-CZ-4860 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5462 
        6.77       107.54         5.46        79.53        90.54        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5986 TCGA-CZ-5988 
       21.76        84.30        22.52         1.94        12.26        22.78 
TCGA-DV-5565 TCGA-DV-5574 TCGA-DV-5575 TCGA-G6-A8L8 TCGA-MM-A563 
       13.28        66.28        56.84        35.87        19.43 

$`8P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 
       38.99        37.38        48.82        62.01        31.07        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 
       51.25        10.49        74.63        74.76        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.64        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 
       15.39        22.65         0.10        11.18        10.62       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 
       73.08       109.41        15.78        73.68       112.08        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        78.64        49.28        94.29        83.21        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 
       22.45        37.58        82.45        72.89        12.13         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         2.53         3.48        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         7.82         2.14        57.70         6.64         3.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 
       15.72        46.59         5.52        33.50        16.77        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        68.71        45.30 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        10.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       26.07        29.03        36.85        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 
       11.90         7.30        25.32        18.51        15.09         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 
        2.24        21.86        52.08        15.95        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       15.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5378 
       31.30        31.66        24.82        32.98        21.57         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.10         0.85         0.53         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       16.80        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5550 
       50.14        23.74         1.18        24.23        16.60        48.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        8.42        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       85.51        94.72        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 
        0.43        89.36        23.05        77.03        62.24        54.90 
TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
       97.45        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4349 
       15.16         0.07        74.17        54.77        49.08        12.23 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       61.68        10.82         5.33        61.97        13.51        56.91 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
       60.95        48.95        36.53        20.38        36.39        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.71        47.97        63.62        58.68        60.30        61.22 
TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       58.98        48.89        49.38         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        18.51        38.70        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 
       52.27        62.86        74.40        49.15        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 
      106.16        54.61        11.05        83.97        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 
       74.27        75.06       116.84        61.91        64.18        30.64 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
      115.69        26.93        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 
       56.35        47.67        49.97        49.18        50.33        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5675 
       45.14         3.06         4.57        18.81       131.08       129.40 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
      133.71        18.87        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 
       73.35        67.00        53.42        62.66       119.64        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
        0.59        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5455 
       93.04        61.41        63.42        58.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 
       79.63        91.69        55.33        94.45        10.85        69.96 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       14.63        62.63        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.96        23.01        16.37        11.70 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.10              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           118.85            149.16 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            38.40             38.56 
[1] "0.1 - 118.8 (38.4)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED        60       14        38       25
  8P LOSS WILD-TYPE     203       43        87       58
D56V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                60               203
  STAGE II               14                43
  STAGE III              38                87
  STAGE IV               25                58
[1] 4 2
[1] TRUE
[1] "dimension of 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    61  16  57   3
  8P LOSS WILD-TYPE 207  53 123   8
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              61               207
  T2              16                53
  T3              57               123
  T4               3                 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"
D56V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    56   4
  8P LOSS WILD-TYPE 178  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     56    4
  8P LOSS WILD-TYPE  178   13
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              56               178
  1               4                13
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   108  25
  8P LOSS WILD-TYPE 310  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    108   25
  8P LOSS WILD-TYPE  310   53
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             108               310
  1              25                53
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    39  98
  8P LOSS WILD-TYPE 150 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     39   98
  8P LOSS WILD-TYPE  150  241
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              39               150
  MALE                98               241
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       3                         9   123
  8P LOSS WILD-TYPE     5                        47   334
D56V11, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   3                 5
  BLACK OR AFRICAN AMERICAN               9                47
  WHITE                                 123               334
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    11  82
  8P LOSS WILD-TYPE  15 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11   82
  8P LOSS WILD-TYPE   15  268
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                15
  NOT HISPANIC OR LATINO              82               268
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    44  20
  8Q LOSS WILD-TYPE 307 155
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               64               462 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               155 
$`8Q LOSS MUTATED`
TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-A6NN TCGA-AK-3426 TCGA-AK-3440 
       28.70        24.16        53.29         0.10        29.10        94.19 
TCGA-AK-3458 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4821 
       38.40        40.70         3.62        58.45         0.59        40.44 
TCGA-B0-4822 TCGA-B0-4845 TCGA-B0-4945 TCGA-B0-5696 TCGA-B4-5838 TCGA-B8-5164 
       36.53        65.29        70.52        85.78         5.46         0.85 
TCGA-B8-5545 TCGA-B8-5549 TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4351 
       50.14         6.38        18.48        62.86        44.94        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4960 
       11.31        12.33        60.59        68.38        15.78        71.41 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5177 
        6.74        57.40        45.50        43.00        37.02         9.63 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4876 TCGA-CJ-4885 
       34.95        31.27       114.41       105.37        64.27       113.46 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 
       51.52        63.98        27.65       109.84        51.25       108.56 
TCGA-CJ-4907 TCGA-CJ-5679 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6088 TCGA-CW-6090 
       49.28        22.32        53.26        75.58       105.93        83.90 
TCGA-CZ-4860 TCGA-CZ-4862 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5463 TCGA-CZ-5465 
        6.77       107.54        79.53        90.54        21.76        84.30 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5575 TCGA-MM-A563 
       12.26        22.78        56.84        19.43 

$`8Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.63        74.76        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3427 
       22.65         0.10        11.18        10.62       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
      109.51        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 
       94.29        83.21        28.73        22.45        37.58        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       72.89        12.13         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 
        2.53         3.48        28.47        19.00         1.38        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 
        6.64         3.25        15.72        46.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 
       45.07        33.50        16.77         6.02        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 
       39.45        26.07        29.03         2.27        36.85        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       70.68        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        0.53         4.64         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       24.23        16.60        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4349 
       93.99        52.24        74.17        54.77        49.08        12.23 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       61.68        10.82         5.33        61.97        13.51        56.91 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        60.95        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       87.45        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 
       58.98        14.24        48.89        49.38         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.74        74.20        30.64        52.27 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      106.16        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        66.21        61.91        57.83        64.18        30.64 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
      115.69        26.93        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       56.35        47.67        49.97        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
       72.00       129.40       133.71        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15       122.83        62.10        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
       74.66         1.35       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
        0.59        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 
       93.04         5.46        61.41        63.42        58.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        79.63        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       10.22        69.96        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5989 
       12.69        80.19        67.96        65.65        14.63        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       66.28        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.96        23.01        16.37        11.70 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.10              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           114.41            149.16 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            45.22             37.43 
[1] "0.1 - 114.4 (45.2)" "0.1 - 149.2 (37.4)"
[1] "hr=" "1.2"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED        28        7        19       10
  8Q LOSS WILD-TYPE     235       50       106       73
D57V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                28               235
  STAGE II                7                50
  STAGE III              19               106
  STAGE IV               10                73
[1] 4 2
[1] TRUE
[1] "dimension of 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    27   7  28   2
  8Q LOSS WILD-TYPE 241  62 152   9
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              27               241
  T2               7                62
  T3              28               152
  T4               2                 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"
D57V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    26   2
  8Q LOSS WILD-TYPE 208  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     26    2
  8Q LOSS WILD-TYPE  208   15
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              26               208
  1               2                15
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    53   9
  8Q LOSS WILD-TYPE 365  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     53    9
  8Q LOSS WILD-TYPE  365   69
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              53               365
  1               9                69
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    14  50
  8Q LOSS WILD-TYPE 175 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     14   50
  8Q LOSS WILD-TYPE  175  289
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              14               175
  MALE                50               289
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                19 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5550        TCGA-B8-A54E        TCGA-B8-A54F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4VX        TCGA-DV-A4W0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-T7-A92I 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D57V10, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                11 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5550        TCGA-DV-A4W0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-MM-A84U        TCGA-T7-A92I 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       1                         3    59
  8Q LOSS WILD-TYPE     7                        53   398
D57V11, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                53
  WHITE                                  59               398
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  35
  8Q LOSS WILD-TYPE  20 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   35
  8Q LOSS WILD-TYPE   20  315
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                20
  NOT HISPANIC OR LATINO              35               315
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    76  72
  9P LOSS WILD-TYPE 275 103
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              148               378 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               72               103 
$`9P LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 
       36.82        39.16        49.08        49.02        37.15        38.47 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 
        4.50        52.93        18.44        24.16        18.87       109.91 
TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AS-3777 TCGA-B0-4688 
       29.10       109.51        78.64        49.28        40.70         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        1.41         4.57         3.48        19.73        57.70        43.96 
TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       46.59        52.21        33.50         6.02        40.44        36.53 
TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5094 
       10.09        40.70        56.68        65.29        29.03        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 
        8.05         2.24        21.86        52.08        62.89        30.48 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5402 TCGA-B0-5694 TCGA-B0-5701 
       38.63        41.88        48.82        42.41        15.78        80.91 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 
       31.66        21.57         5.10         5.46        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4167 
       20.91         6.38         0.53        90.28        32.61        89.36 
TCGA-BP-4176 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       64.27        74.17        62.86        31.89        11.31        12.33 
TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4797 
       41.75        48.07        13.15        68.38        11.64        36.39 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       10.98         6.71        71.41        58.68        60.30        61.22 
TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 
       45.50        31.30        25.81        43.00        45.07        18.51 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 
       36.23        28.87         6.35        30.64        62.86        74.40 
TCGA-BP-5183 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 
       42.44        27.02        31.79        33.47        19.82        31.27 
TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 
       46.55        14.17        79.66        66.21        51.52       115.69 
TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 
       26.93        39.45        56.35        47.67        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 
       54.48        38.56         4.57       131.08       133.71        25.71 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       22.32        25.25       122.83        53.26       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5588 
       75.58        62.66         7.36        64.57         5.39        66.31 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
       83.90        18.77        46.16        47.08        69.21         6.77 
TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
       79.63        10.85        10.22        84.30        22.52         1.94 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5576 TCGA-DV-A4W0 
       31.10        67.96        65.65        14.63        23.90        81.21 
TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A84U 
        7.96        70.13        19.43        23.01 

$`9P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 
       12.66        11.90        47.21         0.53        24.16        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 
       34.29        31.07        45.53        29.92        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68       112.08        68.61        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       48.36        40.01        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 
       37.58        38.40        82.45        72.89        12.13         1.41 
TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        2.53        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        7.82         5.98         2.14         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 
       15.72         0.59         5.52        45.07        16.77        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 
       54.48        29.10        78.44        68.71        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
       53.88         6.71        10.52        10.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5099 
       11.90         7.30        25.32        18.51        15.09        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.87        90.48        52.54        58.59        19.30        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 
       52.73        52.87        51.02        38.43        46.39        56.98 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
      111.52       112.80       129.67       133.94        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       119.38       126.28        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.30        24.82        32.98        16.67        12.00         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.85         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       25.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       50.14        16.60        48.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        61.78        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       44.94        12.23        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4769 
       77.98        77.62         5.98        44.15        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 
       60.95        15.78        48.95        36.53        20.38        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 
       36.95        47.97         6.94        87.45        63.62        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
        5.82        30.64        41.62        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        48.10        79.30         1.74        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 
       52.27         9.63        49.15        38.30        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        34.95         0.95       115.00        63.25        73.22 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        49.25        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
      116.84        64.27        71.87        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       64.18        30.64        63.98        50.01        24.66        27.65 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
      109.84        50.24        49.97        51.25       108.56        49.18 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 
       45.14         3.06        18.81        72.00       129.40        18.87 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 
       18.15        62.10        73.35        67.00       119.64        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 
      105.93       103.43        25.45         0.59        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
      107.54        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5470 
       55.33        94.45        21.76        69.96         2.40        12.69 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       80.19        12.26        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       10.29        35.87         2.01        19.96        16.37        11.70 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.53              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           133.71            149.16 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           38.595            38.350 
[1] "0.5 - 133.7 (38.6)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.9"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED        53       11        49       36
  9P LOSS WILD-TYPE     210       46        76       47
D58V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                53               210
  STAGE II               11                46
  STAGE III              49                76
  STAGE IV               36                47
[1] 4 2
[1] TRUE
[1] "dimension of 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    56  15  73   5
  9P LOSS WILD-TYPE 212  54 107   6
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              56               212
  T2              15                54
  T3              73               107
  T4               5                 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"
D58V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    60   8
  9P LOSS WILD-TYPE 174   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     60    8
  9P LOSS WILD-TYPE  174    9
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              60               174
  1               8                 9
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   109  35
  9P LOSS WILD-TYPE 309  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    109   35
  9P LOSS WILD-TYPE  309   43
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             109               309
  1              35                43
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    37 112
  9P LOSS WILD-TYPE 152 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     37  112
  9P LOSS WILD-TYPE  152  227
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              37               152
  MALE               112               227
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       1                        10   134
  9P LOSS WILD-TYPE     7                        46   323
D58V11, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN              10                46
  WHITE                                 134               323
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     6 100
  9P LOSS WILD-TYPE  20 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6  100
  9P LOSS WILD-TYPE   20  250
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                20
  NOT HISPANIC OR LATINO             100               250
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    79  70
  9Q LOSS WILD-TYPE 272 105
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              149               377 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               70               105 
$`9Q LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 
       36.82        39.16        49.08        49.02        37.15        38.47 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 
        4.50        52.93        18.44        24.16        18.87       109.91 
TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3456 TCGA-AS-3777 
       29.10       109.51        78.64        49.28        37.58        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        1.41         4.57         3.48        19.73        57.70        43.96 
TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       46.59        52.21        33.50         6.02        40.44        36.53 
TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5094 
       10.09        40.70        56.68        65.29        29.03        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 
        8.05         2.24        21.86        52.08        62.89        30.48 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5402 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5701 
       38.63        41.88        42.41        15.78        85.78        80.91 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 
       31.66        21.57         5.10         5.46        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4167 
       20.91         6.38         0.53        90.28        32.61        89.36 
TCGA-BP-4176 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       64.27        74.17        62.86        31.89        11.31        12.33 
TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4797 
       41.75        13.15        68.38        11.64        15.78        36.39 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       10.98         6.71        71.41        58.68        60.30        61.22 
TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 
       45.50        31.30        25.81        43.00        45.07        18.51 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 
       36.23        28.87         6.35        30.64        62.86        74.40 
TCGA-BP-5183 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 
       42.44        27.02        31.79        33.47        19.82        31.27 
TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4876 
       46.55        14.17        21.24        79.66        74.27        64.27 
TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 
       66.21        51.52       115.69        26.93        39.45        56.35 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 
       47.67        49.28        50.33        54.48        38.56         4.57 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
      131.08       133.71        25.71        22.32        25.25       122.83 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 
       53.26       118.85        53.42        75.58        62.66         7.36 
TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 
       64.57         5.39        66.31        83.90        18.77        47.08 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 
       69.21         6.77        58.82        79.63        10.85        10.22 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
       84.30        22.52        31.10        67.96        65.65        14.63 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A84U 
       23.90        81.21        70.13        19.43        23.01 

$`9Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 
       12.66        11.90        47.21         0.53        24.16        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 
       34.29        31.07        45.53        29.92        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68       112.08        68.61        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       48.36        40.01        94.29        83.21        28.73        22.45 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4688 
       38.40        82.45        72.89        12.13         1.41         3.32 
TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        2.53        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        7.82         5.98         2.14         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 
       15.72         0.59         5.52        45.07        16.77        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 
       54.48        29.10        78.44        68.71        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
       53.88         6.71        10.52        10.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5099 
       11.90         7.30        25.32        18.51        15.09        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.87        90.48        52.54        58.59        19.30        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
       56.98       111.52       112.80       129.67       133.94        70.68 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       119.38       126.28        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.30        24.82        32.98        16.67        12.00         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.85         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       25.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       50.14        16.60        48.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        61.78        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       44.94        12.23        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62         5.98        44.15        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 
       56.91        60.95        48.95        36.53        20.38        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 
       36.95        47.97         6.94        87.45        63.62        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
        5.82        30.64        41.62        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        48.10        79.30         1.74        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 
       52.27         9.63        49.15        38.30        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        34.95         0.95       115.00        63.25        73.22 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 
       83.97        49.25        10.72        75.06       116.84        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 
       61.91        57.83       113.46        64.18        30.64        63.98 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 
       50.01        24.66        27.65       109.84        50.24        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 
       51.25       108.56        49.18        45.14         3.06        18.81 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       72.00       129.40        18.87        18.15        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
       67.00       119.64        92.02        81.83        85.78        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35       105.93       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       46.16         0.59        58.75        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        61.41        63.42        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 
       18.44        90.54        91.69        55.33        94.45        21.76 
TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 
       69.96         2.40         1.94        12.69        80.19        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4VX TCGA-DV-A4VZ 
       11.67        37.15        66.28        56.84        53.46        12.00 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.96        16.37        11.70 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.53              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           133.71            149.16 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            38.63             38.30 
[1] "0.5 - 133.7 (38.6)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.7"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED        50       14        51       35
  9Q LOSS WILD-TYPE     213       43        74       48
D59V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                50               213
  STAGE II               14                43
  STAGE III              51                74
  STAGE IV               35                48
[1] 4 2
[1] TRUE
[1] "dimension of 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    52  18  76   4
  9Q LOSS WILD-TYPE 216  51 104   7
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              52               216
  T2              18                51
  T3              76               104
  T4               4                 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"
D59V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    63   8
  9Q LOSS WILD-TYPE 171   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     63    8
  9Q LOSS WILD-TYPE  171    9
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              63               171
  1               8                 9
[1] 2 2
[1] FALSE
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   111  34
  9Q LOSS WILD-TYPE 307  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    111   34
  9Q LOSS WILD-TYPE  307   44
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             111               307
  1              34                44
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    37 113
  9Q LOSS WILD-TYPE 152 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     37  113
  9Q LOSS WILD-TYPE  152  226
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              37               152
  MALE               113               226
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
D59V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       1                        10   135
  9Q LOSS WILD-TYPE     7                        46   322
D59V11, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN              10                46
  WHITE                                 135               322
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     8  99
  9Q LOSS WILD-TYPE  18 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   99
  9Q LOSS WILD-TYPE   18  251
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                18
  NOT HISPANIC OR LATINO              99               251
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    43  24
  10P LOSS WILD-TYPE 308 151
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                67                459 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                24                151 
$`10P LOSS MUTATED`
TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-A6NN TCGA-AK-3433 
        4.50        18.44        43.20        18.64         0.10       112.08 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4688 
       94.19        46.78        38.40        72.89        12.13         3.32 
TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4828 
       28.47         3.62        43.96        46.59         6.02        10.09 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-5117 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5835 
       10.52        65.29        52.87        32.61        21.57         0.53 
TCGA-B8-4143 TCGA-B8-5549 TCGA-B8-5550 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4166 
       23.31         6.38        48.53        90.28        32.61         0.43 
TCGA-BP-4334 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4770 TCGA-BP-4775 
       21.21        62.86        31.89        11.31        10.82        60.59 
TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 
       36.39         6.71        71.41        45.50        31.30        43.00 
TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 
        6.35         1.74        33.47        19.82        31.27        46.55 
TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 
       75.06        61.91        24.66       109.84        47.67        49.28 
TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5460 
       18.81       133.71        83.90         6.77        90.54        94.45 
TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-DV-5566 TCGA-EU-5907 
       84.30        31.10        12.69        80.19        45.96         4.18 
TCGA-G6-A8L8 
       35.87 

$`10P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       34.29        31.07        52.93        45.53        29.92        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 
       74.76        24.16        53.29        55.76        20.71        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       48.36        78.64        40.01        49.28        94.29        83.21 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3777 TCGA-AS-3778 
       28.73        22.45        37.58        82.45        40.70         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         2.53         3.48        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 
        6.64         3.25        58.45        15.72         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 
       52.21        45.07        33.50        16.77        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       14.93        54.48        29.10        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4844 
       45.30        27.42        53.88         6.71        56.68        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       41.88        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46       126.05        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 
       16.67        12.00         5.75         5.10         0.85         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        5.46         0.36         0.23        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       50.14        16.60         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 
        3.58        27.78        62.07        80.68        37.25        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        74.17        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       61.97        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
       36.95        47.97         6.94        87.45        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       14.24        48.89        49.38         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 
       37.48        35.21        36.23        28.87        48.10        79.30 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       24.62        44.55        34.95         0.95       115.00        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       10.72        74.27       116.84        64.27        71.87        66.21 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
      115.69        26.93        50.01        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       56.35        49.97        51.25       108.56        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 
       54.48        38.56        45.14         3.06         4.57       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00       129.40        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 
       66.31        78.18        74.66         1.35       105.93       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       79.63        91.69        55.33        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5985 
       69.96        22.52         2.40         1.94        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5567 
       12.26        14.63        22.78        62.63        13.28        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       53.46        12.00        81.21        18.12         3.91         6.77 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        70.13         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.10               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            133.71             149.16 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             32.61              38.99 
[1] "0.1 - 133.7 (32.6)" "0.1 - 149.2 (39.0)"
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED        25        6        23       13
  10P LOSS WILD-TYPE     238       51       102       70
D60V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                 25                238
  STAGE II                 6                 51
  STAGE III               23                102
  STAGE IV                13                 70
[1] 4 2
[1] TRUE
[1] "dimension of 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    25   7  31   4
  10P LOSS WILD-TYPE 243  62 149   7
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               25                243
  T2                7                 62
  T3               31                149
  T4                4                  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"
D60V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    30   0
  10P LOSS WILD-TYPE 204  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     30    0
  10P LOSS WILD-TYPE  204   17
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               30                204
  1                0                 17
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    53  12
  10P LOSS WILD-TYPE 365  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     53   12
  10P LOSS WILD-TYPE  365   66
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               53                365
  1               12                 66
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    20  47
  10P LOSS WILD-TYPE 169 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20   47
  10P LOSS WILD-TYPE  169  292
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               20                169
  MALE                 47                292
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
[1] "Remove cluster labels:" "10P LOSS MUTATED"      
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                 20 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-4621         TCGA-B8-5158 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54E         TCGA-B8-A54F 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-DV-A4VX 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
D60V10, continuous
[1] "Remove cluster labels:" "10P LOSS MUTATED"      
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                 11 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A563 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-MM-A84U         TCGA-T7-A92I 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         5    59
  10P LOSS WILD-TYPE     8                        51   398
D60V11, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                5                 51
  WHITE                                   59                398
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     5  39
  10P LOSS WILD-TYPE  21 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      5   39
  10P LOSS WILD-TYPE   21  311
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 21
  NOT HISPANIC OR LATINO               39                311
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    58  31
  10Q LOSS WILD-TYPE 293 144
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                89                437 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                31                144 
$`10Q LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3331 TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 
       49.08        48.82         4.50        18.44        43.20        18.64 
TCGA-A3-A6NN TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3458 TCGA-AK-3461 
        0.10       112.08        94.19        46.78        38.40        72.89 
TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4712 
       12.13         3.32         1.41        28.47         3.62        43.96 
TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4837 
       58.45        46.59         6.02        10.09        40.70        45.30 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-5099 TCGA-B0-5117 TCGA-B0-5402 
       10.52        10.29        65.29        15.95        52.87        42.41 
TCGA-B0-5703 TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5835 TCGA-B4-5838 
       73.84       105.37        32.61        21.57         0.53         5.46 
TCGA-B8-4143 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4164 
       23.31         6.38        48.53        16.27        90.28        32.61 
TCGA-BP-4166 TCGA-BP-4329 TCGA-BP-4334 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 
        0.43        27.78        21.21        74.17        62.86        31.89 
TCGA-BP-4766 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 
       48.07        10.82        60.59        36.39         6.71        71.41 
TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5180 
       45.50        31.30        43.00         6.35         1.74        74.40 
TCGA-BP-5185 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4642 
       37.22        33.47        19.82        31.27        46.55       105.37 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 
       10.72        75.06        61.91        24.66       109.84        47.67 
TCGA-CJ-4907 TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-6090 
       49.28        18.81       133.71       119.64         7.36        83.90 
TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 
        6.77        90.54        94.45        84.30        31.10        12.69 
TCGA-CZ-5982 TCGA-DV-5565 TCGA-DV-5566 TCGA-EU-5907 TCGA-G6-A8L8 
       80.19        13.28        45.96         4.18        35.87 

$`10Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.99        38.47        37.38        62.01        34.29        31.07 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       52.93        45.53        29.92        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       53.29        55.76        20.71        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        33.47        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       15.78        73.68        68.61       109.51        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 
       37.58        82.45        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        3.48        19.00         1.38        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 
        2.14        19.73        57.70         6.64         3.25        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       40.44        36.53        14.93        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4846 
       68.71        27.42        53.88         6.71        56.68        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        66.05        38.63        52.73        41.88        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
       38.43        48.82        46.39        56.98       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 
      119.38       126.28        80.91        71.41       149.16       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       79.89       131.15        89.49        91.46       126.05        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       32.98        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.36         0.23        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       50.14        16.60         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 
       15.42        14.17       111.02        85.51        94.72       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       93.34        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        37.25        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        54.77        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       13.15        61.68         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 
       20.38        10.98        37.25        36.95        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       87.45        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       28.87        48.10        79.30        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        62.86        49.15        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       13.41        24.62        44.55        34.95         0.95       115.00 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 
       74.27       116.84        64.27        71.87        66.21        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       26.93        50.01        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.25       108.56        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 
       38.56        45.14         3.06         4.57       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      129.40        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       53.42        75.58        62.66        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35       105.93       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        79.63        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        69.96        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        1.94        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       62.63        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       56.84        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
        3.91         6.77         7.96        10.29        70.13         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.10               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            133.71             149.16 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             36.39              38.63 
[1] "0.1 - 133.7 (36.4)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED        34       11        26       18
  10Q LOSS WILD-TYPE     229       46        99       65
D61V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                 34                229
  STAGE II                11                 46
  STAGE III               26                 99
  STAGE IV                18                 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"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED    34  12  37   6
  10Q LOSS WILD-TYPE 234  57 143   5
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               34                234
  T2               12                 57
  T3               37                143
  T4                6                  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"
D61V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    38   1
  10Q LOSS WILD-TYPE 196  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     38    1
  10Q LOSS WILD-TYPE  196   16
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               38                196
  1                1                 16
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    71  15
  10Q LOSS WILD-TYPE 347  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     71   15
  10Q LOSS WILD-TYPE  347   63
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               71                347
  1               15                 63
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    25  64
  10Q LOSS WILD-TYPE 164 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     25   64
  10Q LOSS WILD-TYPE  164  275
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               25                164
  MALE                 64                275
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-4621         TCGA-B8-5158 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54E         TCGA-B8-A54F 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-DV-A4VX 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D61V10, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                 11 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A563 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MM-A84U         TCGA-T7-A92I 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         6    80
  10Q LOSS WILD-TYPE     8                        50   377
D61V11, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                6                 50
  WHITE                                   80                377
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6  54
  10Q LOSS WILD-TYPE  20 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   54
  10Q LOSS WILD-TYPE   20  296
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               54                296
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     8  10
  11P LOSS WILD-TYPE 343 165
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                508 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                10                165 
$`11P LOSS MUTATED`
TCGA-A3-3316 TCGA-AK-3465 TCGA-B0-4696 TCGA-B0-4707 TCGA-B0-4819 TCGA-B0-4822 
       49.08        12.13        28.47        19.73         6.02        36.53 
TCGA-B0-5084 TCGA-B0-5702 TCGA-B2-5641 TCGA-B4-5838 TCGA-BP-4352 TCGA-BP-4768 
        7.30        71.41        21.57         5.46        11.31        13.15 
TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5201 TCGA-CW-5588 TCGA-CZ-5465 TCGA-CZ-5469 
       31.30         1.74        31.27        66.31        84.30        31.10 

$`11P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       72.89        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        2.53         3.48        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        7.82         5.98         2.14        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4823 
       52.21        45.07        33.50        16.77        40.44        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
      126.28        80.91        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       24.82        32.98        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.85         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 
       24.62        33.47        19.82        44.55        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        69.96        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.00        81.21        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1.74               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             84.30             149.16 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            25.020             39.075 
[1] "1.7 - 84.3 (25.0)"  "0.1 - 149.2 (39.1)"
[1] "hr=" "2.5"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         6        3         4        5
  11P LOSS WILD-TYPE     257       54       121       78
D62V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  6                257
  STAGE II                 3                 54
  STAGE III                4                121
  STAGE IV                 5                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED     6   3   9   0
  11P LOSS WILD-TYPE 262  66 171  11
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                6                262
  T2                3                 66
  T3                9                171
  T4                0                 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"
D62V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     8   2
  11P LOSS WILD-TYPE 226  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8    2
  11P LOSS WILD-TYPE  226   15
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                8                226
  1                2                 15
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    14   4
  11P LOSS WILD-TYPE 404  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     14    4
  11P LOSS WILD-TYPE  404   74
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               14                404
  1                4                 74
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     6  12
  11P LOSS WILD-TYPE 183 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6   12
  11P LOSS WILD-TYPE  183  327
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                6                183
  MALE                 12                327
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       0                         1    16
  11P LOSS WILD-TYPE     8                        55   441
D62V11, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   16                441
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  13
  11P LOSS WILD-TYPE  26 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   13
  11P LOSS WILD-TYPE   26  337
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               13                337
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    11  12
  11Q LOSS WILD-TYPE 340 163
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                503 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                12                163 
$`11Q LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3346 TCGA-AK-3425 TCGA-AK-3465 TCGA-B0-4696 TCGA-B0-4707 
       49.08         4.50       109.91        12.13        28.47        19.73 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-5084 TCGA-B0-5702 TCGA-B2-5641 TCGA-B4-5832 
        6.02        36.53         7.30        71.41        21.57         5.10 
TCGA-B4-5838 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-5173 
        5.46        11.31        13.15        31.30        25.81         1.74 
TCGA-BP-5201 TCGA-CW-5588 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
       31.27        66.31        84.30         1.94        31.10 

$`11Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       31.07        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
      112.08        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       78.64        40.01        49.28        94.29        83.21        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 
       22.45        37.58        38.40        82.45        72.89        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        2.14        57.70        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77        40.44        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         5.75         0.85         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       53.65        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       34.95         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        69.96        22.52 
TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        2.40        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       53.46        12.00        81.21        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1.74               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            109.91             149.16 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             21.57              39.45 
[1] "1.7 - 109.9 (21.6)" "0.1 - 149.2 (39.5)"
[1] "hr=" "2.4"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         9        3         5        6
  11Q LOSS WILD-TYPE     254       54       120       77
D63V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  9                254
  STAGE II                 3                 54
  STAGE III                5                120
  STAGE IV                 6                 77
[1] 4 2
[1] TRUE
[1] "dimension of 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     9   3  11   0
  11Q LOSS WILD-TYPE 259  66 169  11
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                9                259
  T2                3                 66
  T3               11                169
  T4                0                 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"
D63V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    11   2
  11Q LOSS WILD-TYPE 223  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     11    2
  11Q LOSS WILD-TYPE  223   15
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               11                223
  1                2                 15
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    18   5
  11Q LOSS WILD-TYPE 400  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     18    5
  11Q LOSS WILD-TYPE  400   73
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               18                400
  1                5                 73
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6  17
  11Q LOSS WILD-TYPE 183 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6   17
  11Q LOSS WILD-TYPE  183  322
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                6                183
  MALE                 17                322
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
D63V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       0                         1    21
  11Q LOSS WILD-TYPE     8                        55   436
D63V11, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   21                436
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  16
  11Q LOSS WILD-TYPE  25 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   16
  11Q LOSS WILD-TYPE   25  334
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               16                334
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     4   0
  12P LOSS WILD-TYPE 347 175
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                522 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                175 
$`12P LOSS MUTATED`
TCGA-BP-4166 TCGA-BP-4775 TCGA-CZ-5457 TCGA-T7-A92I 
        0.43        60.59        90.54        11.70 

$`12P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       94.19        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        31.66        24.82        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         0.85         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       13.15        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        79.63        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       56.84        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.43               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             90.54             149.16 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            36.145             38.450 
[1] "0.4 - 90.5 (36.1)"  "0.1 - 149.2 (38.5)"
[1] "hr="     "3300000"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         2        0         2        0
  12P LOSS WILD-TYPE     261       57       123       83
D64V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  2                261
  STAGE II                 0                 57
  STAGE III                2                123
  STAGE IV                 0                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED     2   0   2   0
  12P LOSS WILD-TYPE 266  69 178  11
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                2                266
  T2                0                 69
  T3                2                178
  T4                0                 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"
D64V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1   0
  12P LOSS WILD-TYPE 233  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    0
  12P LOSS WILD-TYPE  233   17
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                1                233
  1                0                 17
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3   0
  12P LOSS WILD-TYPE 415  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE  415   78
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                3                415
  1                0                 78
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2   2
  12P LOSS WILD-TYPE 187 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    2
  12P LOSS WILD-TYPE  187  337
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                187
  MALE                  2                337
[1] 2 2
[1] FALSE
D64V8, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 51 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4861         TCGA-CZ-4862 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5458         TCGA-CZ-5465 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4VX 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-A4VZ         TCGA-DV-A4W0         TCGA-EU-5904 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D64V9, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 20 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-4621         TCGA-B8-5158 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-5550         TCGA-B8-A54E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-A4VX         TCGA-DV-A4W0         TCGA-G6-A5PC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D64V10, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 11 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-5550         TCGA-DV-A4W0         TCGA-G6-A8L7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-MM-A84U 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         1     3
  12P LOSS WILD-TYPE     8                        55   454
D64V11, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                    3                454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0   2
  12P LOSS WILD-TYPE  26 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    2
  12P LOSS WILD-TYPE   26  348
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                2                348
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     3   1
  12Q LOSS WILD-TYPE 348 174
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                522 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                174 
$`12Q LOSS MUTATED`
TCGA-B0-5095 TCGA-BP-4166 TCGA-BP-4775 TCGA-CZ-5457 
        8.05         0.43        60.59        90.54 

$`12Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       94.19        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 
        7.30        25.32        18.51        15.09        10.95         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       61.68        10.82         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.74        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        79.63        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.43               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             90.54             149.16 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             34.32              38.45 
[1] "0.4 - 90.5 (34.3)"  "0.1 - 149.2 (38.5)"
[1] "hr=" "1.2"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         1        0         3        0
  12Q LOSS WILD-TYPE     262       57       122       83
D65V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                262
  STAGE II                 0                 57
  STAGE III                3                122
  STAGE IV                 0                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED     1   0   3   0
  12Q LOSS WILD-TYPE 267  69 177  11
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                267
  T2                0                 69
  T3                3                177
  T4                0                 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"
D65V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2   0
  12Q LOSS WILD-TYPE 232  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    0
  12Q LOSS WILD-TYPE  232   17
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                2                232
  1                0                 17
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     4   0
  12Q LOSS WILD-TYPE 414  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4    0
  12Q LOSS WILD-TYPE  414   78
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                4                414
  1                0                 78
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1   3
  12Q LOSS WILD-TYPE 188 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    3
  12Q LOSS WILD-TYPE  188  336
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                1                188
  MALE                  3                336
[1] 2 2
[1] FALSE
D65V8, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4861         TCGA-CZ-4862 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5458         TCGA-CZ-5465 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4VX 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-A4VZ         TCGA-DV-A4W0         TCGA-EU-5904 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"12Q LOSS WILD-TYPE" 
D65V9, continuous
D65V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0     4
  12Q LOSS WILD-TYPE     8                        56   453
D65V11, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 56
  WHITE                                    4                453
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0   2
  12Q LOSS WILD-TYPE  26 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    2
  12Q LOSS WILD-TYPE   26  348
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                2                348
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    36  34
  13Q LOSS WILD-TYPE 315 141
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                70                456 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                34                141 
$`13Q LOSS MUTATED`
TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3370 TCGA-A3-3374 TCGA-AK-3426 
       37.15         4.50        52.93        74.76        43.20        29.10 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 
      112.08        94.19        78.64        12.13        40.70         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 
        1.41         4.57        28.47         1.38         3.62        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       43.96        52.21         6.02        15.09        10.95         8.05 
TCGA-B0-5113 TCGA-B0-5117 TCGA-B0-5696 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       38.63        52.87        85.78         5.10         0.53         5.46 
TCGA-B8-5163 TCGA-B8-5549 TCGA-BP-4167 TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4343 
       27.02         6.38        89.36        21.21        93.99        62.86 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4964 
       11.31        33.99        13.15        10.82        15.78        61.22 
TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5175 
       57.40        45.50        31.30        43.00        37.02        30.64 
TCGA-BP-5191 TCGA-CJ-4868 TCGA-CJ-4881 TCGA-CJ-4901 TCGA-CJ-5677 TCGA-CJ-5679 
       31.79        21.24        66.21        47.67        25.71        22.32 
TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4860 
       53.42        66.31        83.90        18.77        46.16         6.77 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5465 TCGA-CZ-5468 
       63.39        61.41        18.44        90.54        84.30         1.94 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-5568 TCGA-G6-A8L7 
       31.10        67.96        12.16        70.13 

$`13Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       31.07        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 
       82.32        51.25        10.49        28.70        74.63        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       53.29        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        0.10        11.18        10.62       109.91       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
      109.41        15.78        73.68        68.61       109.51        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        40.01        49.28        94.29        83.21        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       22.45        37.58        38.40        82.45        72.89         1.41 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        2.53         3.48        19.00        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       40.44        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       15.78        70.68        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67        12.00         5.75         0.85 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       50.14        20.91        23.74         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        0.43        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 
       80.68        37.25        15.16         0.07        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       74.17        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       12.33        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        60.95        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 
       87.45        71.41        63.62        58.68        60.30        61.51 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 
        6.74        58.98        14.24        48.89        49.38         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30         1.74        74.20        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 
       37.22        22.78        13.35        27.02        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06       116.84        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        49.97        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26       118.85        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 
       73.18        78.18        74.66         1.35       105.93       103.43 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       25.45         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
      107.54        93.04         5.46        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       23.74        79.63        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 
       10.22        21.76        69.96        22.52         2.40        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       13.28        45.96        65.88        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       56.84        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.53               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            112.08             149.16 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            31.545             39.075 
[1] "0.5 - 112.1 (31.5)" "0.1 - 149.2 (39.1)"
[1] "hr=" "1.8"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED        25        2        24       20
  13Q LOSS WILD-TYPE     238       55       101       63
D66V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 25                238
  STAGE II                 2                 55
  STAGE III               24                101
  STAGE IV                20                 63
[1] 4 2
[1] TRUE
[1] "dimension of 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    27   3  34   7
  13Q LOSS WILD-TYPE 241  66 146   4
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               27                241
  T2                3                 66
  T3               34                146
  T4                7                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    34   4
  13Q LOSS WILD-TYPE 200  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     34    4
  13Q LOSS WILD-TYPE  200   13
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               34                200
  1                4                 13
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    52  17
  13Q LOSS WILD-TYPE 366  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     52   17
  13Q LOSS WILD-TYPE  366   61
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               52                366
  1               17                 61
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    22  49
  13Q LOSS WILD-TYPE 167 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     22   49
  13Q LOSS WILD-TYPE  167  290
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               22                167
  MALE                 49                290
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 19 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-4146 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B8-4621         TCGA-B8-5158         TCGA-B8-5164 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B8-5550         TCGA-B8-A54E         TCGA-B8-A54F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-DV-A4VX 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-MM-A563 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"13Q LOSS WILD-TYPE" 
D66V10, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 10 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3451 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-B8-5550 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-MM-A563         TCGA-MM-A84U 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"13Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         4    66
  13Q LOSS WILD-TYPE     8                        52   391
D66V11, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                4                 52
  WHITE                                   66                391
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  49
  13Q LOSS WILD-TYPE  25 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   49
  13Q LOSS WILD-TYPE   25  301
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               49                301
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   123  92
  14Q LOSS WILD-TYPE 228  83
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               215                311 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                92                 83 
$`14Q LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       36.82        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3324 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3351 
       38.99        62.01        34.29         4.50        52.93        29.92 
TCGA-A3-3357 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 TCGA-A3-A6NI TCGA-AK-3426 
       88.37        20.71        18.87        20.28        33.47        29.10 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3450 TCGA-AK-3451 
      117.80       109.41        15.78       109.51        49.28        94.29 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4703 
       28.73        22.45        38.40         4.57         3.48         5.98 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4817 
       19.73        43.96         6.64         5.52        52.21        33.50 
TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
        6.02        10.09        78.44        40.70        27.42        53.88 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5081 
       26.07        29.03        36.85        70.52        20.94        11.90 
TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5106 
        7.30        15.09        10.95         2.24        21.86        52.54 
TCGA-B0-5107 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5694 TCGA-B0-5697 
       30.48        38.63        56.98       129.67        15.78        86.47 
TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-4098 
      119.38        80.91        79.89       131.15        89.49         1.68 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 
       31.30        31.66        24.82        32.98        21.57         5.10 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-5158 
        4.64         5.46         0.36        23.31        17.19        20.91 
TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5553 TCGA-B8-A54D 
        1.18         0.85        48.53         0.53        14.30        27.29 
TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4173 
        1.74         4.93        93.34        32.61        89.36        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4331 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       61.78        64.27        80.68        62.86        49.08        44.94 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4768 
       11.31        12.33        33.99         5.98        41.75        13.15 
TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 
        5.33        56.91        68.38        15.78        36.39        10.98 
TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4965 TCGA-BP-4970 TCGA-BP-4971 
        6.71        87.45        58.68        61.51        14.24        48.89 
TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4989 
       45.50        14.93        36.07        46.45        25.81         3.88 
TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 
       16.47        18.51        37.02        36.23         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5183 
        1.74        74.20        30.64        62.86        74.40        42.44 
TCGA-BP-5185 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 
       37.22        27.02        33.24        31.79        33.47        19.82 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       31.27        63.25        73.22        14.17       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 
      105.37        11.05        21.24        83.97        79.66        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4888 
       75.06       116.84        64.27        66.21        57.83        51.52 
TCGA-CJ-4891 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 
       26.93        24.66        27.65       109.84        51.25        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-4923 
       50.33        54.48        38.56        45.14         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       22.32        25.25       122.83        67.00        53.26       118.85 
TCGA-CJ-6030 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 
       75.58         7.36        64.57         5.39        73.18        66.31 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4860 
        1.35        83.90        18.77        46.16        69.21         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5455 
       14.66        63.39        93.04        61.41        58.82        18.44 
TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5468 
       79.63        10.85        10.22        21.76        84.30         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5989 
       31.10        12.69        67.96        65.65        14.63        62.63 
TCGA-DV-5573 TCGA-DV-A4VX TCGA-G6-A5PC TCGA-MM-A563 TCGA-MM-A84U 
       37.15        53.46         7.96        19.43        23.01 

$`14Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3322 
       12.66        11.90        47.21         0.53        24.16        48.59 
TCGA-A3-3323 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 
       36.36        38.47        37.38        48.82        31.07        45.53 
TCGA-A3-3352 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       18.44        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       18.64        28.31        65.52        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3431 
        0.10        11.18        10.62       109.91        73.08        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
      112.08        68.61        94.19        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       40.01        83.21        37.58        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4696 
       40.70         1.41         3.32         1.41         2.53        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 
       19.00         1.38         3.62        65.10         7.82         2.14 
TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
       57.70         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       45.07        16.77        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       29.10        68.71        45.30         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4849 TCGA-B0-5077 TCGA-B0-5080 
       10.29        65.29        39.45         2.27        43.30        11.24 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       25.32        18.51         8.05        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       90.87        90.48        58.59        19.30        66.05        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
       42.41       111.52       112.80       133.94        70.68        85.78 
TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
      126.28        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
       91.46       126.05        32.61        35.90        31.96        21.30 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5844 
       16.67        12.00         5.75         0.85         0.53         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        27.16        42.71        25.05        45.37        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 
       25.91        50.14        23.74        27.02        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54H 
       16.60         6.38        34.39        29.88        17.06         8.42 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       94.72        90.28       101.06        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       77.03        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4351 
       18.48        52.24        74.17        54.77        12.23        31.89 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       31.33        12.30        72.59        77.98        77.62        44.15 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 
       71.80        48.07        61.68        10.82        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       13.51        11.64        60.95        48.95        36.53        20.38 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       37.25        36.95        47.97         6.94        71.41        63.62 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4972 
       60.30        61.22         6.74        57.40        58.98        49.38 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 
        6.90        47.11        53.65        33.34        31.30        36.95 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       27.22        46.45         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       41.62        38.70        27.62        37.48        35.21        28.87 
TCGA-BP-5168 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 
       48.10        52.27         9.63        49.15        38.30        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 
       22.78        13.35        23.47        13.41        24.62        44.55 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4643 
       34.95         0.95       115.00        46.55       106.16        58.95 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 
       49.25        10.72        71.87        61.91       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 
       30.64        63.98       115.69        50.01        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4918 
       56.35        47.67        49.97       108.56        49.18         3.06 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       18.15        62.10        73.35        53.42        62.66       119.64 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
       92.02        81.83        85.78        78.18        74.66       105.93 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4862 
      103.43        25.45         0.59        47.08        58.75       107.54 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5457 TCGA-CZ-5458 
        5.46        63.42        79.53        23.74        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5982 
       55.33        94.45        69.96        22.52         2.40        80.19 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       12.26        22.78        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 
       11.67        66.28        56.84        23.90        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         3.91         6.77         4.18        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.96        16.37        11.70 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.36               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            133.71             149.16 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             36.23              41.88 
[1] "0.4 - 133.7 (36.2)" "0.1 - 149.2 (41.9)"
[1] "hr=" "1.7"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        80       26        63       47
  14Q LOSS WILD-TYPE     183       31        62       36
D67V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 80                183
  STAGE II                26                 31
  STAGE III               63                 62
  STAGE IV                47                 36
[1] 4 2
[1] TRUE
[1] "dimension of 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    85  34  94   3
  14Q LOSS WILD-TYPE 183  35  86   8
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               85                183
  T2               34                 35
  T3               94                 86
  T4                3                  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"
D67V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    93  14
  14Q LOSS WILD-TYPE 141   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     93   14
  14Q LOSS WILD-TYPE  141    3
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               93                141
  1               14                  3
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   162  46
  14Q LOSS WILD-TYPE 256  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    162   46
  14Q LOSS WILD-TYPE  256   32
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              162                256
  1               46                 32
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    65 151
  14Q LOSS WILD-TYPE 124 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     65  151
  14Q LOSS WILD-TYPE  124  188
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               65                124
  MALE                151                188
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
D67V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       2                        14   196
  14Q LOSS WILD-TYPE     6                        42   261
D67V11, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN               14                 42
  WHITE                                  196                261
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    12 147
  14Q LOSS WILD-TYPE  14 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12  147
  14Q LOSS WILD-TYPE   14  203
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 14
  NOT HISPANIC OR LATINO              147                203
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    17  19
  15Q LOSS WILD-TYPE 334 156
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                36                490 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                19                156 
$`15Q LOSS MUTATED`
TCGA-A3-3319 TCGA-A3-3382 TCGA-B0-4690 TCGA-B0-4698 TCGA-B0-4712 TCGA-B0-4821 
       37.15        18.87         1.41         1.38        43.96        40.44 
TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5116 TCGA-B4-5832 TCGA-B8-4620 
       11.24         7.30         8.05        41.88         5.10        25.55 
TCGA-B8-5549 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4768 
        6.38        32.61        89.36        62.86        11.31        13.15 
TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-4985 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 
       60.59        36.39        31.30         6.35        30.64        62.86 
TCGA-BP-5200 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5677 TCGA-CJ-6028 TCGA-CZ-4857 
       34.95        47.67        49.28        25.71        53.42        47.08 
TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-G6-A8L8 
        6.77        90.54        10.85        31.10        67.96        35.87 

$`15Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.64        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       73.68       112.08        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       48.36        78.64        40.01        49.28        94.29        83.21 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         3.32         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        5.98         2.14        19.73        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5085 
       36.85        70.52        20.94        43.30        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       18.51        15.09        10.95         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 
       58.59        19.30        66.05        38.63        52.73        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
      111.52       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         5.75         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 
       27.16        42.71        25.05        45.37        17.19        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        50.14        16.60        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       85.51        94.72        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        0.43        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       80.68        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        74.17        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        20.38        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       28.87        48.10        79.30         1.74        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        50.24        56.35        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
      108.56        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
      133.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       62.10        73.35        67.00        53.26       118.85        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
       46.16         0.59        69.21        58.75        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        79.63        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
        2.40         1.94        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       53.46        12.00        81.21        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        70.13         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.38               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             90.54             149.16 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            31.955             39.075 
[1] "1.4 - 90.5 (32.0)"  "0.1 - 149.2 (39.1)"
[1] "hr=" "2.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         9        2        13       12
  15Q LOSS WILD-TYPE     254       55       112       71
D68V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  9                254
  STAGE II                 2                 55
  STAGE III               13                112
  STAGE IV                12                 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"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED    10   2  21   3
  15Q LOSS WILD-TYPE 258  67 159   8
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               10                258
  T2                2                 67
  T3               21                159
  T4                3                  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"
D68V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    17   1
  15Q LOSS WILD-TYPE 217  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     17    1
  15Q LOSS WILD-TYPE  217   16
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               17                217
  1                1                 16
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    24  11
  15Q LOSS WILD-TYPE 394  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     24   11
  15Q LOSS WILD-TYPE  394   67
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               24                394
  1               11                 67
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     8  28
  15Q LOSS WILD-TYPE 181 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8   28
  15Q LOSS WILD-TYPE  181  311
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                8                181
  MALE                 28                311
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       1                         1    34
  15Q LOSS WILD-TYPE     7                        55   423
D68V11, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                1                 55
  WHITE                                   34                423
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0  22
  15Q LOSS WILD-TYPE  26 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   22
  15Q LOSS WILD-TYPE   26  328
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               22                328
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     5   5
  16P LOSS WILD-TYPE 346 170
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                516 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                170 
$`16P LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-A6NN TCGA-B0-4696 TCGA-B0-4822 TCGA-B8-5551 TCGA-BP-4354 
       49.08         0.10        28.47        36.53         0.53        33.99 
TCGA-BP-4770 TCGA-BP-4797 TCGA-BP-4985 TCGA-CZ-5982 
       10.82        36.39        31.30        80.19 

$`16P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       33.47        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       73.68       112.08        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       48.36        78.64        40.01        49.28        94.29        83.21 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       12.13        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        2.53         3.48        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       40.44        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
      111.52       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
       48.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        12.33        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        20.38        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.74        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        31.10        12.69        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.10               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             80.19             149.16 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            32.645             38.665 
[1] "0.1 - 80.2 (32.6)"  "0.1 - 149.2 (38.7)"
[1] "hr=" "2.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         3        2         3        2
  16P LOSS WILD-TYPE     260       55       122       81
D69V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  3                260
  STAGE II                 2                 55
  STAGE III                3                122
  STAGE IV                 2                 81
[1] 4 2
[1] TRUE
[1] "dimension of 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     3   2   3   2
  16P LOSS WILD-TYPE 265  67 177   9
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                3                265
  T2                2                 67
  T3                3                177
  T4                2                  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"
D69V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     5   1
  16P LOSS WILD-TYPE 229  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    1
  16P LOSS WILD-TYPE  229   16
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                5                229
  1                1                 16
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     8   1
  16P LOSS WILD-TYPE 410  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      8    1
  16P LOSS WILD-TYPE  410   77
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                8                410
  1                1                 77
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3   7
  16P LOSS WILD-TYPE 186 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    7
  16P LOSS WILD-TYPE  186  332
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                186
  MALE                  7                332
[1] 2 2
[1] FALSE
D69V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 52 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4861         TCGA-CZ-4862 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-DV-5565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4VX 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-A4VZ         TCGA-DV-A4W0         TCGA-EU-5904 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"16P LOSS WILD-TYPE" 
D69V9, continuous
D69V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         2     8
  16P LOSS WILD-TYPE     8                        54   449
D69V11, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 54
  WHITE                                    8                449
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   5
  16P LOSS WILD-TYPE  26 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    5
  16P LOSS WILD-TYPE   26  345
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                5                345
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     9   7
  16Q LOSS WILD-TYPE 342 168
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                510 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                168 
$`16Q LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-A6NN TCGA-B0-4822 TCGA-B0-4836 TCGA-B0-4837 
       36.82        49.08         0.10        36.53        40.70        45.30 
TCGA-B0-5097 TCGA-B0-5402 TCGA-B8-5551 TCGA-BP-4354 TCGA-BP-4770 TCGA-BP-4797 
       21.86        42.41         0.53        33.99        10.82        36.39 
TCGA-BP-4985 TCGA-CZ-5982 TCGA-G6-A8L8 TCGA-MM-A564 
       31.30        80.19        35.87        19.96 

$`16Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        47.21         0.53        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.47        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       15.39        22.65         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
      112.08        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       78.64        40.01        49.28        94.29        83.21        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       40.44        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       68.71        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60         6.38        48.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       80.68        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        12.33        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        20.38        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.74        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       70.13         2.01        19.43        23.01        16.37        11.70 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.10               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             80.19             149.16 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            36.130             38.665 
[1] "0.1 - 80.2 (36.1)"  "0.1 - 149.2 (38.7)"
[1] "hr=" "1.8"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         6        3         3        4
  16Q LOSS WILD-TYPE     257       54       122       79
D70V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  6                257
  STAGE II                 3                 54
  STAGE III                3                122
  STAGE IV                 4                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     6   3   4   3
  16Q LOSS WILD-TYPE 262  66 176   8
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                6                262
  T2                3                 66
  T3                4                176
  T4                3                  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"
D70V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     7   1
  16Q LOSS WILD-TYPE 227  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    1
  16Q LOSS WILD-TYPE  227   16
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                7                227
  1                1                 16
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    11   2
  16Q LOSS WILD-TYPE 407  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     11    2
  16Q LOSS WILD-TYPE  407   76
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               11                407
  1                2                 76
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5  11
  16Q LOSS WILD-TYPE 184 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   11
  16Q LOSS WILD-TYPE  184  328
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                5                184
  MALE                 11                328
[1] 2 2
[1] FALSE
D70V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4861         TCGA-CZ-4862 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5458 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-DV-5565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4VX 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-A4VZ         TCGA-DV-A4W0         TCGA-EU-5904 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-T7-A92I 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D70V9, continuous
D70V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         4    12
  16Q LOSS WILD-TYPE     8                        52   445
D70V11, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                4                 52
  WHITE                                   12                445
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     0  11
  16Q LOSS WILD-TYPE  26 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0   11
  16Q LOSS WILD-TYPE   26  339
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               11                339
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    28  18
  17P LOSS WILD-TYPE 323 157
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                480 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                18                157 
$`17P LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 
       49.08        37.15         4.50        43.20        18.87       112.08 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
      109.51        94.19        40.01        37.58        12.13        40.70 
TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4813 TCGA-B0-4817 TCGA-B0-4833 
        3.62        19.73        43.96         0.59        33.50        78.44 
TCGA-B0-4836 TCGA-B0-5117 TCGA-B0-5702 TCGA-B2-3923 TCGA-B4-5835 TCGA-BP-4166 
       40.70        52.87        71.41        32.61         0.53         0.43 
TCGA-BP-4334 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 
       21.21        31.89        11.31        15.78        36.39        10.98 
TCGA-BP-4994 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-5676 
       43.00        33.47        19.82        79.66        10.72       133.71 
TCGA-CJ-5677 TCGA-CW-5588 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5460 TCGA-CZ-5465 
       25.71        66.31        69.21         6.77        94.45        84.30 
TCGA-CZ-5468 TCGA-DV-5565 TCGA-DV-A4VX TCGA-G6-A8L7 
        1.94        13.28        53.46        70.13 

$`17P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       24.16        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.47        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       24.16        53.29        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 
       73.08       109.41        15.78        73.68        68.61        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        78.64        49.28        94.29        83.21        28.73 
TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       22.45        38.40        82.45        72.89         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        1.38        65.10         7.82         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 
        6.64         3.25        58.45        15.72        46.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       52.21        45.07        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4837 
       14.93        54.48        29.10        10.09        68.71        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       80.91        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46       126.05        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        32.61        99.85        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 
        3.58        27.78        62.07        80.68        37.25        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        60.95        48.95        36.53        20.38 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.74        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       13.41        24.62        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       83.97        49.25        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 
       18.81       131.08        72.00       129.40        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 
       79.63        90.54        91.69        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       21.76        69.96        22.52         2.40        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       62.63        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       66.28        56.84        23.90        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.43               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            133.71             149.16 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            36.770             38.595 
[1] "0.4 - 133.7 (36.8)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.3"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED        17        6        11       12
  17P LOSS WILD-TYPE     246       51       114       71
D71V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                 17                246
  STAGE II                 6                 51
  STAGE III               11                114
  STAGE IV                12                 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"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED    17   7  20   2
  17P LOSS WILD-TYPE 251  62 160   9
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               17                251
  T2                7                 62
  T3               20                160
  T4                2                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    20   0
  17P LOSS WILD-TYPE 214  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     20    0
  17P LOSS WILD-TYPE  214   17
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               20                214
  1                0                 17
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    32  12
  17P LOSS WILD-TYPE 386  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     32   12
  17P LOSS WILD-TYPE  386   66
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               32                386
  1               12                 66
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    12  34
  17P LOSS WILD-TYPE 177 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     12   34
  17P LOSS WILD-TYPE  177  305
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               12                177
  MALE                 34                305
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 19 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-4621         TCGA-B8-5158 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-5550         TCGA-B8-A54E 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-MM-A563 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"17P LOSS WILD-TYPE" 
D71V10, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                 11 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B8-5550         TCGA-DV-A4W0         TCGA-MM-A563 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-MM-A84U         TCGA-T7-A92I 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         5    40
  17P LOSS WILD-TYPE     8                        51   417
D71V11, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                5                 51
  WHITE                                   40                417
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  31
  17P LOSS WILD-TYPE  25 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   31
  17P LOSS WILD-TYPE   25  319
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               31                319
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    20   8
  17Q LOSS WILD-TYPE 331 167
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                28                498 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                167 
$`17Q LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3436 
       49.08        37.15         4.50        43.20       112.08       109.51 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4712 
       94.19        40.01        12.13        40.70         3.62        43.96 
TCGA-B0-4817 TCGA-B0-4836 TCGA-B0-5117 TCGA-B2-3923 TCGA-BP-4166 TCGA-BP-4334 
       33.50        40.70        52.87        32.61         0.43        21.21 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4797 TCGA-BP-4994 TCGA-BP-5196 TCGA-CJ-4871 
       31.89        11.31        36.39        43.00        33.47        79.66 
TCGA-CJ-5676 TCGA-CW-5588 TCGA-CZ-5460 TCGA-CZ-5465 
      133.71        66.31        94.45        84.30 

$`17Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       24.16        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.47        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        49.28        94.29        83.21 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         1.38        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        2.14        19.73        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        68.71        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       41.88        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46       126.05        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        32.61        99.85        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 
       62.86        54.77        49.08        44.94        12.23        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.74        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 
       33.24        31.79        23.47        13.41        24.62        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95       115.00        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      105.37        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
      131.08        72.00       129.40        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        69.96        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.43               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            133.71             149.16 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             40.70              38.35 
[1] "0.4 - 133.7 (40.7)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED        10        4         7        7
  17Q LOSS WILD-TYPE     253       53       118       76
D72V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                 10                253
  STAGE II                 4                 53
  STAGE III                7                118
  STAGE IV                 7                 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"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED    10   5  12   1
  17Q LOSS WILD-TYPE 258  64 168  10
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               10                258
  T2                5                 64
  T3               12                168
  T4                1                 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"
D72V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    10   0
  17Q LOSS WILD-TYPE 224  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    0
  17Q LOSS WILD-TYPE  224   17
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               10                224
  1                0                 17
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    21   7
  17Q LOSS WILD-TYPE 397  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21    7
  17Q LOSS WILD-TYPE  397   71
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               21                397
  1                7                 71
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     7  21
  17Q LOSS WILD-TYPE 182 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   21
  17Q LOSS WILD-TYPE  182  318
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                7                182
  MALE                 21                318
[1] 2 2
[1] FALSE
D72V8, continuous
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4861         TCGA-CZ-4862 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4VX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-A4VZ         TCGA-DV-A4W0         TCGA-EU-5904 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"17Q LOSS WILD-TYPE" 
D72V9, continuous
D72V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         2    25
  17Q LOSS WILD-TYPE     8                        54   432
D72V11, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 54
  WHITE                                   25                432
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  18
  17Q LOSS WILD-TYPE  25 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   18
  17Q LOSS WILD-TYPE   25  332
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               18                332
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    50  42
  18P LOSS WILD-TYPE 301 133
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                92                434 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                42                133 
$`18P LOSS MUTATED`
TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3387 
       37.15         4.50        52.93        88.37        24.16        20.28 
TCGA-AK-3425 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3465 TCGA-B0-4698 
      109.91        15.78       109.51        94.19        12.13         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 
        3.62        65.10         5.98        19.73        43.96         6.64 
TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4827 
       46.59        52.21         6.02        40.44        36.53        29.10 
TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5092 TCGA-B0-5097 
       40.70        10.29        65.29        29.03        15.09        21.86 
TCGA-B2-4098 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4620 TCGA-B8-4621 
        1.68        21.57         5.10         0.53        25.55        25.91 
TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4338 
       27.02         6.38        48.53        32.61         0.43        93.99 
TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4756 TCGA-BP-4761 
       18.48        62.86        11.31        12.33        12.30         5.98 
TCGA-BP-4770 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4962 TCGA-BP-4977 
       10.82        68.38        36.39         6.71        58.68        14.93 
TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 
       31.30        43.00        18.51         6.35        30.64        62.86 
TCGA-BP-5181 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 
       49.15        31.79        33.47        19.82        34.95        31.27 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4888 
       63.25        73.22        74.27        66.21        61.91        51.52 
TCGA-CJ-4891 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4920 TCGA-CJ-5677 TCGA-CJ-5679 
       26.93        47.67        49.28         4.57        25.71        22.32 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
      118.85        53.42        66.31        47.08        69.21         6.77 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5985 
       63.39        61.41        79.63         1.94        67.96        65.65 
TCGA-CZ-5988 TCGA-MM-A84U 
       22.78        23.01 

$`18P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3358 TCGA-A3-3359 
       31.07        45.53        29.92        18.44        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       43.20        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62        29.10       117.80        73.08       109.41 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68       112.08        68.61        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 
       37.58        38.40        82.45        72.89        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
       19.00         7.82         2.14        57.70         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       15.72         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 
       14.93        54.48        10.09        78.44        68.71        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 
       27.42        53.88         6.71        56.68        10.52        39.45 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5094 
       11.24        11.90         7.30        25.32        18.51        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
      126.05        32.61        35.90        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        24.82        32.98        16.67        12.00         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.85         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       50.14        20.91        23.74         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       50.14        16.60         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
       90.28       101.06        93.34        99.85        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 
       21.21        15.16         0.07        52.24        74.17        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        31.89        33.99        31.33 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98        77.62        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 
       36.53        20.38        10.98        37.25        36.95        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 
        6.94        87.45        71.41        63.62        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 
       49.38        45.50         6.90        47.11        53.65        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       28.87        48.10        79.30         1.74        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       22.78        13.35        27.02        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 
       24.62        44.55         0.95       115.00        46.55        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 
       21.24        83.97        49.25        79.66        10.72        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
      116.84        64.27        71.87        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       30.64        63.98       115.69        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        50.24        56.35        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
      108.56        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        3.06        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       67.00        53.26        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        46.16         0.59        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
      107.54        93.04         5.46        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5987 
        2.40        31.10        12.69        80.19        12.26        14.63 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       81.21        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.43               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            118.85             149.16 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            31.285             39.730 
[1] "0.4 - 118.8 (31.3)" "0.1 - 149.2 (39.7)"
[1] "hr=" "1.8"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED        31        7        33       22
  18P LOSS WILD-TYPE     232       50        92       61
D73V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                 31                232
  STAGE II                 7                 50
  STAGE III               33                 92
  STAGE IV                22                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    33   9  46   5
  18P LOSS WILD-TYPE 235  60 134   6
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               33                235
  T2                9                 60
  T3               46                134
  T4                5                  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"
D73V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    42   3
  18P LOSS WILD-TYPE 192  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     42    3
  18P LOSS WILD-TYPE  192   14
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               42                192
  1                3                 14
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    71  20
  18P LOSS WILD-TYPE 347  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     71   20
  18P LOSS WILD-TYPE  347   58
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               71                347
  1               20                 58
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    28  65
  18P LOSS WILD-TYPE 161 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     28   65
  18P LOSS WILD-TYPE  161  274
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               28                161
  MALE                 65                274
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 19 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-5158         TCGA-B8-5164 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B8-A54E         TCGA-B8-A54F         TCGA-B8-A54G 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-DV-A4VX         TCGA-DV-A4W0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G6-A5PC         TCGA-G6-A8L7         TCGA-MM-A563 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"18P LOSS WILD-TYPE" 
D73V10, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 10 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A563 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"18P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       2                         6    85
  18P LOSS WILD-TYPE     6                        50   372
D73V11, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                6                 50
  WHITE                                   85                372
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1  62
  18P LOSS WILD-TYPE  25 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   62
  18P LOSS WILD-TYPE   25  288
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               62                288
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    53  41
  18Q LOSS WILD-TYPE 298 134
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                94                432 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                41                134 
$`18Q LOSS MUTATED`
TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3372 
       24.16        37.15         4.50        52.93        88.37        24.16 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3465 
       20.28       109.91        15.78       109.51        94.19        12.13 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4712 TCGA-B0-4713 
        1.38         3.62        65.10         5.98        43.96         6.64 
TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4836 
       52.21         6.02        40.44        36.53        29.10        40.70 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5092 TCGA-B0-5097 TCGA-B0-5121 
       10.29        65.29        29.03        15.09        21.86        48.82 
TCGA-B2-4098 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4620 TCGA-B8-4621 
        1.68        21.57         5.10         0.53        25.55        25.91 
TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4338 
       27.02         6.38        48.53        32.61         0.43        93.99 
TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4770 
       62.86        11.31        12.33        12.30         5.98        10.82 
TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4962 TCGA-BP-4977 TCGA-BP-4985 
       68.38        36.39         6.71        58.68        14.93        31.30 
TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5181 
       43.00        18.51         6.35        30.64        62.86        49.15 
TCGA-BP-5182 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 
       38.30        31.79        33.47        19.82        34.95        31.27 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4888 
       63.25        73.22        10.72        74.27        66.21        51.52 
TCGA-CJ-4891 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4920 TCGA-CJ-5677 TCGA-CJ-5679 
       26.93        47.67        49.28         4.57        25.71        22.32 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5588 TCGA-CZ-4854 TCGA-CZ-4857 
      118.85        53.42       119.64        66.31        46.16        47.08 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5468 
       69.21         6.77        63.39        61.41        79.63         1.94 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5988 TCGA-MM-A84U 
       67.96        65.65        22.78        23.01 

$`18Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.08        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.47        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        18.44        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
       10.62        29.10       117.80        73.08       109.41        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      112.08        68.61        46.78        48.36        78.64        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       38.40        82.45        72.89        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
        7.82         2.14        19.73        57.70         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       16.77        14.93        54.48        10.09        78.44        68.71 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       38.43        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
      126.05        32.61        35.90        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        24.82        32.98        16.67        12.00         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.85         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       50.14        20.91        23.74         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       50.14        16.60         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
       90.28       101.06        93.34        99.85        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       21.21        15.16         0.07        18.48        52.24        74.17 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 
       31.33        72.59        77.98        77.62        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        61.68         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       60.59        13.51        56.91        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        20.38        10.98        37.25        36.95 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 
       47.97         6.94        87.45        71.41        63.62        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       36.23        28.87        48.10        79.30         1.74        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       52.27         9.63        74.40        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       22.78        13.35        27.02        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 
       24.62        44.55         0.95       115.00        46.55        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        79.66        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       30.64        63.98       115.69        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        50.24        56.35        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
      108.56        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        3.06        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.26        75.58        62.66         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4864 
       25.45         0.59        58.75        14.66       107.54        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 
       21.76        69.96        84.30        22.52         2.40        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5565 
       12.69        80.19        12.26        14.63        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       56.84        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.43               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            119.64             149.16 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            31.545             39.730 
[1] "0.4 - 119.6 (31.5)" "0.1 - 149.2 (39.7)"
[1] "hr=" "1.7"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED        35        8        30       22
  18Q LOSS WILD-TYPE     228       49        95       61
D74V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 35                228
  STAGE II                 8                 49
  STAGE III               30                 95
  STAGE IV                22                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED    37  10  43   5
  18Q LOSS WILD-TYPE 231  59 137   6
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               37                231
  T2               10                 59
  T3               43                137
  T4                5                  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"
D74V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    45   3
  18Q LOSS WILD-TYPE 189  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     45    3
  18Q LOSS WILD-TYPE  189   14
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               45                189
  1                3                 14
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    73  20
  18Q LOSS WILD-TYPE 345  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     73   20
  18Q LOSS WILD-TYPE  345   58
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               73                345
  1               20                 58
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    28  67
  18Q LOSS WILD-TYPE 161 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     28   67
  18Q LOSS WILD-TYPE  161  272
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               28                161
  MALE                 67                272
[1] 2 2
[1] FALSE
D74V8, continuous
D74V9, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 19 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-5158         TCGA-B8-5164 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B8-A54E         TCGA-B8-A54F         TCGA-B8-A54G 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-DV-A4VX         TCGA-DV-A4W0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G6-A5PC         TCGA-G6-A8L7         TCGA-MM-A563 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"18Q LOSS WILD-TYPE" 
D74V10, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 10 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A563 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"18Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       2                         6    87
  18Q LOSS WILD-TYPE     6                        50   370
D74V11, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                6                 50
  WHITE                                   87                370
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2  63
  18Q LOSS WILD-TYPE  24 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   63
  18Q LOSS WILD-TYPE   24  287
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               63                287
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     2   9
  19P LOSS WILD-TYPE 349 166
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                515 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 9                166 
$`19P LOSS MUTATED`
TCGA-A3-3319 TCGA-AK-3425 TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4707 TCGA-B0-4821 
       37.15       109.91         1.41        28.47        19.73        40.44 
TCGA-B0-4828 TCGA-BP-4164 TCGA-BP-4770 TCGA-BP-4985 TCGA-CZ-4860 
       10.09        32.61        10.82        31.30         6.77 

$`19P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       10.62        29.10       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       73.68       112.08        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       48.36        78.64        40.01        49.28        94.29        83.21 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         3.32         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        3.48        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        5.98         2.14        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       85.51        94.72        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       61.68         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
       53.65        14.93        36.07        33.34        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.74        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61       105.37        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66       107.54        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       53.46        12.00        81.21        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              1.41               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            109.91             149.16 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             28.47              38.70 
[1] "1.4 - 109.9 (28.5)" "0.1 - 149.2 (38.7)"
[1] "hr=" "3.8"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         2        0         5        4
  19P LOSS WILD-TYPE     261       57       120       79
D75V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  2                261
  STAGE II                 0                 57
  STAGE III                5                120
  STAGE IV                 4                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED     2   1   5   3
  19P LOSS WILD-TYPE 266  68 175   8
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                2                266
  T2                1                 68
  T3                5                175
  T4                3                  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"
D75V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     6   0
  19P LOSS WILD-TYPE 228  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6    0
  19P LOSS WILD-TYPE  228   17
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                6                228
  1                0                 17
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     8   3
  19P LOSS WILD-TYPE 410  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8    3
  19P LOSS WILD-TYPE  410   75
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                8                410
  1                3                 75
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3   8
  19P LOSS WILD-TYPE 186 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    8
  19P LOSS WILD-TYPE  186  331
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                3                186
  MALE                  8                331
[1] 2 2
[1] FALSE
D75V8, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 52 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4VX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-A4VZ         TCGA-DV-A4W0         TCGA-EU-5904 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"19P LOSS WILD-TYPE" 
D75V9, continuous
D75V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         0    10
  19P LOSS WILD-TYPE     7                        56   447
D75V11, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 56
  WHITE                                   10                447
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0   6
  19P LOSS WILD-TYPE  26 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    6
  19P LOSS WILD-TYPE   26  344
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                6                344
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     1   3
  19Q LOSS WILD-TYPE 350 172
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                522 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                172 
$`19Q LOSS MUTATED`
TCGA-A3-3319 TCGA-B0-4690 TCGA-BP-4164 TCGA-CZ-4860 
       37.15         1.41        32.61         6.77 

$`19Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         3.32         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        2.53         3.48        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       94.72        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       80.68        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       44.94        12.23        31.89        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.74        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1.41               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             37.15             149.16 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            19.690             38.595 
[1] "1.4 - 37.1 (19.7)"  "0.1 - 149.2 (38.6)"
[1] "hr=" "4.9"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         1        0         1        2
  19Q LOSS WILD-TYPE     262       57       124       81
D76V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                262
  STAGE II                 0                 57
  STAGE III                1                124
  STAGE IV                 2                 81
[1] 4 2
[1] TRUE
[1] "dimension of 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     1   0   1   2
  19Q LOSS WILD-TYPE 267  69 179   9
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                267
  T2                0                 69
  T3                1                179
  T4                2                  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"
D76V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1   0
  19Q LOSS WILD-TYPE 233  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    0
  19Q LOSS WILD-TYPE  233   17
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                1                233
  1                0                 17
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2   2
  19Q LOSS WILD-TYPE 416  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    2
  19Q LOSS WILD-TYPE  416   76
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                2                416
  1                2                 76
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1   3
  19Q LOSS WILD-TYPE 188 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    3
  19Q LOSS WILD-TYPE  188  336
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                1                188
  MALE                  3                336
[1] 2 2
[1] FALSE
D76V8, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5465 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4VX 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-A4VZ         TCGA-DV-A4W0         TCGA-EU-5904 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"19Q LOSS WILD-TYPE" 
D76V9, continuous
D76V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     4
  19Q LOSS WILD-TYPE     8                        56   453
D76V11, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 56
  WHITE                                    4                453
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0   1
  19Q LOSS WILD-TYPE  26 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    1
  19Q LOSS WILD-TYPE   26  349
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                1                349
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     5   3
  20P LOSS WILD-TYPE 346 172
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                518 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                172 
$`20P LOSS MUTATED`
TCGA-A3-3319 TCGA-B0-4821 TCGA-BP-4352 TCGA-BP-4962 TCGA-BP-5000 TCGA-BP-5182 
       37.15        40.44        11.31        58.68        18.51        38.30 
TCGA-BP-5184 TCGA-CJ-4637 
       37.25        73.22 

$`20P LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       72.89        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 
       47.97         6.94        87.45        71.41        63.62        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
       43.00        45.07        30.64        41.62        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.74        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5185 
        9.63        62.86        74.40        49.15        42.44        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 
       31.27         0.95       115.00        46.55        63.25        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             11.31               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             73.22             149.16 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            37.775             38.515 
[1] "11.3 - 73.2 (37.8)" "0.1 - 149.2 (38.5)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         4        1         1        2
  20P LOSS WILD-TYPE     259       56       124       81
D77V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  4                259
  STAGE II                 1                 56
  STAGE III                1                124
  STAGE IV                 2                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED     4   2   2   0
  20P LOSS WILD-TYPE 264  67 178  11
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                4                264
  T2                2                 67
  T3                2                178
  T4                0                 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"
D77V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3   0
  20P LOSS WILD-TYPE 231  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    0
  20P LOSS WILD-TYPE  231   17
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                3                231
  1                0                 17
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     6   2
  20P LOSS WILD-TYPE 412  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    2
  20P LOSS WILD-TYPE  412   76
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                6                412
  1                2                 76
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3   5
  20P LOSS WILD-TYPE 186 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    5
  20P LOSS WILD-TYPE  186  334
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                186
  MALE                  5                334
[1] 2 2
[1] FALSE
D77V8, continuous
D77V9, continuous
D77V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       1                         0     7
  20P LOSS WILD-TYPE     7                        56   450
D77V11, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 56
  WHITE                                    7                450
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1   3
  20P LOSS WILD-TYPE  25 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    3
  20P LOSS WILD-TYPE   25  347
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO                3                347
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     2   1
  20Q LOSS WILD-TYPE 349 174
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                523 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                174 
$`20Q LOSS MUTATED`
TCGA-BP-4962 TCGA-BP-5000 TCGA-CJ-4637 
       58.68        18.51        73.22 

$`20Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       94.19        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        31.66        24.82        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         0.85         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       71.41        63.62        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        63.25        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       56.84        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             18.51               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             73.22             149.16 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             58.68              38.43 
[1] "18.5 - 73.2 (58.7)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.2"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         1        1         0        1
  20Q LOSS WILD-TYPE     262       56       125       82
D78V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  1                262
  STAGE II                 1                 56
  STAGE III                0                125
  STAGE IV                 1                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     1   2   0   0
  20Q LOSS WILD-TYPE 267  67 180  11
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                1                267
  T2                2                 67
  T3                0                180
  T4                0                 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"
D78V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   0
  20Q LOSS WILD-TYPE 234  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    0
  20Q LOSS WILD-TYPE  234   17
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   1
  20Q LOSS WILD-TYPE 416  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    1
  20Q LOSS WILD-TYPE  416   77
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                2                416
  1                1                 77
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   2
  20Q LOSS WILD-TYPE 188 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE  188  337
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                188
  MALE                  2                337
[1] 2 2
[1] FALSE
D78V8, continuous
D78V9, continuous
D78V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     3
  20Q LOSS WILD-TYPE     8                        56   454
D78V11, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 56
  WHITE                                    3                454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   0
  20Q LOSS WILD-TYPE  25 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    0
  20Q LOSS WILD-TYPE   25  350
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO                0                350
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    35  20
  21Q LOSS WILD-TYPE 316 155
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                55                471 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                20                155 
$`21Q LOSS MUTATED`
TCGA-A3-3317 TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 
       49.02        43.20       117.80        15.78       112.08        94.19 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4710 
       12.13        40.70         1.38         3.62        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-5084 TCGA-B0-5117 
       43.96        46.59        10.09        68.71         7.30        52.87 
TCGA-B0-5402 TCGA-B0-5695 TCGA-B0-5697 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5553 
       42.41        70.68        86.47         5.46        17.19        14.30 
TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4768 TCGA-BP-4770 
       62.24        97.45        21.21        18.48        13.15        10.82 
TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4983 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5198 
        6.71        71.41        46.45        43.00         6.35        19.82 
TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4913 
       66.21       109.84        47.67        51.25        49.28        38.56 
TCGA-CJ-4923 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-6087 
       18.81        67.00        53.26        53.42        66.31         1.35 
TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-DV-A4VX 
        6.77        90.54        91.69        84.30        22.52        53.46 
TCGA-MM-A563 
       19.43 

$`21Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 
      109.91        29.10        73.08       109.41        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
      109.51        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 
        2.53         3.48        28.47        19.00        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        5.98         2.14         6.64         3.25        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       66.05        38.63        52.73        41.88        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       48.82        46.39        56.98       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
      133.94        15.78        85.78       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.85         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        27.16        42.71        25.05        45.37        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
        0.53        34.39        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       61.78        64.27        54.90        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        37.25        15.16         0.07        93.99 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        48.07        61.68         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
       37.25        36.95        47.97         6.94        87.45        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 
       47.11        53.65        14.93        36.07        33.34        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10        79.30         1.74        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95       115.00        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
       39.45        50.24        56.35        49.97       108.56        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 
       50.33        54.48        45.14         3.06         4.57       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 
       25.25        18.15       122.83        62.10        73.35       118.85 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
       81.83         5.39        85.78        73.18        78.18        74.66 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5459 TCGA-CZ-5460 
       79.53        23.74        18.44        79.63        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        21.76        69.96         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.00        81.21        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 
        7.96        10.29        70.13        35.87         2.01        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.35               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            117.80             149.16 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             43.96              37.38 
[1] "1.4 - 117.8 (44.0)" "0.1 - 149.2 (37.4)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        21        4        17       13
  21Q LOSS WILD-TYPE     242       53       108       70
D79V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 21                242
  STAGE II                 4                 53
  STAGE III               17                108
  STAGE IV                13                 70
[1] 4 2
[1] TRUE
[1] "dimension of 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    20   5  25   5
  21Q LOSS WILD-TYPE 248  64 155   6
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               20                248
  T2                5                 64
  T3               25                155
  T4                5                  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"
D79V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    22   4
  21Q LOSS WILD-TYPE 212  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     22    4
  21Q LOSS WILD-TYPE  212   13
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               22                212
  1                4                 13
[1] 2 2
[1] FALSE
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    45   8
  21Q LOSS WILD-TYPE 373  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     45    8
  21Q LOSS WILD-TYPE  373   70
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               45                373
  1                8                 70
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    17  38
  21Q LOSS WILD-TYPE 172 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     17   38
  21Q LOSS WILD-TYPE  172  301
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               17                172
  MALE                 38                301
[1] 2 2
[1] FALSE
D79V8, continuous
D79V9, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 19 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-4621         TCGA-B8-5158 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-5550         TCGA-B8-A54E 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-T7-A92I 
"21Q LOSS WILD-TYPE" 
D79V10, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                 11 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-5158 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B8-5550         TCGA-DV-A4W0         TCGA-G6-A8L7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-MM-A84U         TCGA-T7-A92I 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         4    47
  21Q LOSS WILD-TYPE     7                        52   410
D79V11, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                4                 52
  WHITE                                   47                410
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2  36
  21Q LOSS WILD-TYPE  24 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   36
  21Q LOSS WILD-TYPE   24  314
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               36                314
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    18  21
  22Q LOSS WILD-TYPE 333 154
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                487 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                21                154 
$`22Q LOSS MUTATED`
TCGA-A3-3347 TCGA-AK-3453 TCGA-AK-3456 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4828 
       52.93        83.21        37.58        19.73        43.96        10.09 
TCGA-B0-4844 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5116 TCGA-B0-5701 
       10.29        15.09        10.95        52.08        41.88        80.91 
TCGA-B2-4098 TCGA-B8-4143 TCGA-B8-A54E TCGA-BP-4343 TCGA-BP-4768 TCGA-BP-4799 
        1.68        23.31        29.88        62.86        13.15        37.25 
TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4992 TCGA-BP-5175 
       71.41         6.74        31.30        25.81        16.47        30.64 
TCGA-BP-5196 TCGA-CJ-4637 TCGA-CJ-4640 TCGA-CJ-4891 TCGA-CJ-4897 TCGA-CJ-4901 
       33.47        73.22       114.41        26.93       109.84        47.67 
TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CW-6097 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 
       53.26        53.42        18.77        61.41        90.54        10.85 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-DV-5566 
        1.94        31.10        45.96 

$`22Q LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       34.29        31.07         4.50        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       28.73        22.45        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       14.93        54.48        29.10        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       25.32        18.51         8.05         2.24        21.86        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       19.30        66.05        38.63        52.73        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       119.38       126.28        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
      126.05        32.61        35.90        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       27.29        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       80.68        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        74.17        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       10.98        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 
       63.62        58.68        60.30        61.22        61.51        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 
       36.95        27.22         3.88        46.45         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30         1.74        74.20        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       23.47        13.41        24.62        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 
       31.27         0.95       115.00        46.55        63.25        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       67.00       118.85        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 
       79.63        91.69        55.33        94.45        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 
       69.96        84.30        22.52         2.40        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       13.28        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       56.84        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              1.68               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            114.41             149.16 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             33.47              38.63 
[1] "1.7 - 114.4 (33.5)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.9"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED        11        4        14       10
  22Q LOSS WILD-TYPE     252       53       111       73
D80V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 11                252
  STAGE II                 4                 53
  STAGE III               14                111
  STAGE IV                10                 73
[1] 4 2
[1] TRUE
[1] "dimension of 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    14   6  19   0
  22Q LOSS WILD-TYPE 254  63 161  11
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               14                254
  T2                6                 63
  T3               19                161
  T4                0                 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"
D80V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    16   1
  22Q LOSS WILD-TYPE 218  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     16    1
  22Q LOSS WILD-TYPE  218   16
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               16                218
  1                1                 16
[1] 2 2
[1] FALSE
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    28  10
  22Q LOSS WILD-TYPE 390  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     28   10
  22Q LOSS WILD-TYPE  390   68
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               28                390
  1               10                 68
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    13  26
  22Q LOSS WILD-TYPE 176 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     13   26
  22Q LOSS WILD-TYPE  176  313
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               13                176
  MALE                 26                313
[1] 2 2
[1] FALSE
D80V8, continuous
D80V9, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-A3-A8CQ         TCGA-A3-A8OV         TCGA-A3-A8OW 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-4621         TCGA-B8-5158 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-5550         TCGA-B8-A54F 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-DV-A4VX 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D80V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       0                         4    35
  22Q LOSS WILD-TYPE     8                        52   422
D80V11, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                4                 52
  WHITE                                   35                422
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     6  23
  22Q LOSS WILD-TYPE  20 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   23
  22Q LOSS WILD-TYPE   20  327
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               23                327
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    27  19
  XP LOSS WILD-TYPE 324 156
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               46               480 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               19               156 
$`XP LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3383 TCGA-AK-3440 TCGA-AK-3447 
       36.82        49.02        37.15        28.31        94.19        40.01 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4813 TCGA-B0-4834 
       12.13        40.70        28.47         3.62         0.59        68.71 
TCGA-B0-4836 TCGA-B0-4845 TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5117 TCGA-B0-5402 
       40.70        65.29         7.30        52.08        52.87        42.41 
TCGA-B0-5705 TCGA-B2-3923 TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-A54D TCGA-BP-4164 
      149.16        32.61        23.74         6.38        27.29        32.61 
TCGA-BP-4327 TCGA-BP-4334 TCGA-BP-4761 TCGA-BP-4959 TCGA-BP-5004 TCGA-BP-5176 
        3.58        21.21         5.98        87.45        37.02        52.27 
TCGA-BP-5180 TCGA-BP-5196 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-5677 TCGA-CJ-5680 
       74.40        33.47       105.37        27.65        25.71        25.25 
TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-5458 TCGA-CZ-5465 TCGA-CZ-5985 TCGA-CZ-5987 
      118.85        83.90        91.69        84.30        65.65        14.63 
TCGA-EU-5907 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U 
        4.18        35.87        19.43        23.01 

$`XP LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       49.08        49.58        48.59        36.36        38.99        38.47 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        62.01        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
      117.80        73.08       109.41        15.78        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        46.78        48.36        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        2.53         3.48        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 
        3.25        58.45        15.72        46.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4837 
       14.93        54.48        29.10        10.09        78.44        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        21.86        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        66.05        38.63        52.73        41.88        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
       38.43        48.82        46.39        56.98       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 
      119.38       126.28        80.91        71.41        73.84       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54F 
       48.53         0.53        34.39        14.30        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       27.78        62.07        80.68        37.25        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
        6.35        79.30         1.74        74.20        30.64         9.63 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       13.41        24.62        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       26.93        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        22.32        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        79.63        90.54        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        69.96        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 
        1.94        31.10        12.69        80.19        67.96        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC 
       12.00        81.21        18.12         3.91         6.77         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       10.29        70.13         2.01        19.96        16.37        11.70 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.59              0.07 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           149.16            133.94 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           36.345            38.665 
[1] "0.6 - 149.2 (36.3)" "0.1 - 133.9 (38.7)"
[1] "hr=" "1.3"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED        22        6        10        8
  XP LOSS WILD-TYPE     241       51       115       75
D81V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                22               241
  STAGE II                6                51
  STAGE III              10               115
  STAGE IV                8                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP LOSS MUTATED    21   6  17   2
  XP LOSS WILD-TYPE 247  63 163   9
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              21               247
  T2               6                63
  T3              17               163
  T4               2                 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"
D81V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    12   2
  XP LOSS WILD-TYPE 222  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     12    2
  XP LOSS WILD-TYPE  222   15
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              12               222
  1               2                15
[1] 2 2
[1] FALSE
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    35   7
  XP LOSS WILD-TYPE 383  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     35    7
  XP LOSS WILD-TYPE  383   71
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              35               383
  1               7                71
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    12  34
  XP LOSS WILD-TYPE 177 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     12   34
  XP LOSS WILD-TYPE  177  305
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              12               177
  MALE                34               305
[1] 2 2
[1] FALSE
D81V8, continuous
D81V9, continuous
[1] "Remove cluster labels:" "XP LOSS MUTATED"       
clus
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                1                20 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4VX 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-DV-A4W0        TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-T7-A92I 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
D81V10, continuous
[1] "Remove cluster labels:" "XP LOSS MUTATED"       
clus
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                2                10 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5550        TCGA-DV-A4W0 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-T7-A92I 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       0                         6    38
  XP LOSS WILD-TYPE     8                        50   419
D81V11, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               6                50
  WHITE                                  38               419
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0  32
  XP LOSS WILD-TYPE  26 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   32
  XP LOSS WILD-TYPE   26  318
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              32               318
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    27  19
  XQ LOSS WILD-TYPE 324 156
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               46               480 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               19               156 
$`XQ LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3382 TCGA-AK-3440 
       36.82        49.02        37.15         4.50        18.87        94.19 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4813 
       78.64        40.01        12.13        40.70        28.47         0.59 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4845 TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5117 
       68.71        40.70        65.29         7.30        52.08        52.87 
TCGA-B0-5402 TCGA-B0-5705 TCGA-B2-3923 TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-A54D 
       42.41       149.16        32.61        23.74         6.38        27.29 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4334 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4770 
       32.61         3.58        21.21        12.30         5.98        10.82 
TCGA-BP-4959 TCGA-BP-5004 TCGA-BP-5180 TCGA-BP-5196 TCGA-CJ-4642 TCGA-CJ-4894 
       87.45        37.02        74.40        33.47       105.37        27.65 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-5465 TCGA-CZ-5985 
       25.71        25.25       118.85        83.90        84.30        65.65 
TCGA-CZ-5987 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-MM-A563 
       14.63         4.18        35.87        19.43 

$`XQ LOSS WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       49.08        49.58        48.59        36.36        38.99        38.47 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
       37.38        48.82        62.01        34.29        31.07        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
      109.51        46.78        48.36        49.28        94.29        83.21 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       58.45        15.72        46.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4837 TCGA-B0-4838 
       54.48        29.10        10.09        78.44        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        10.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       66.05        38.63        52.73        41.88        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       48.82        46.39        56.98       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
      126.28        80.91        71.41        73.84       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       79.89       131.15        89.49        91.46       126.05        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 
       17.19        25.55        25.91        50.14        20.91         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       27.02         0.85        24.23        50.14        16.60        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
        0.53        34.39        14.30        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       61.78        64.27        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        37.25        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       44.94        12.23        31.89        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 
       31.33        72.59        77.98        77.62        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        61.68         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        18.51        38.70        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5181 
       74.20        30.64        52.27         9.63        62.86        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 
      131.08        72.00       129.40       133.71        18.87        22.32 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35       105.93       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        69.96        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5988 
       31.10        12.69        80.19        67.96        12.26        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       81.21        18.12         3.91         6.77         7.96        10.29 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       70.13         2.01        19.96        23.01        16.37        11.70 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.59              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           149.16            133.94 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           34.670            38.845 
[1] "0.6 - 149.2 (34.7)" "0.1 - 133.9 (38.8)"
[1] "hr=" "1.3"
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED        22        6        10        8
  XQ LOSS WILD-TYPE     241       51       115       75
D82V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                22               241
  STAGE II                6                51
  STAGE III              10               115
  STAGE IV                8                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED    21   6  17   2
  XQ LOSS WILD-TYPE 247  63 163   9
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              21               247
  T2               6                63
  T3              17               163
  T4               2                 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"
D82V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    13   2
  XQ LOSS WILD-TYPE 221  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13    2
  XQ LOSS WILD-TYPE  221   15
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              13               221
  1               2                15
[1] 2 2
[1] FALSE
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    37   6
  XQ LOSS WILD-TYPE 381  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     37    6
  XQ LOSS WILD-TYPE  381   72
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              37               381
  1               6                72
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    12  34
  XQ LOSS WILD-TYPE 177 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12   34
  XQ LOSS WILD-TYPE  177  305
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              12               177
  MALE                34               305
[1] 2 2
[1] FALSE
D82V8, continuous
D82V9, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                19 
       TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3451 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-4146        TCGA-B8-4621        TCGA-B8-5158 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E        TCGA-B8-A54F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4VX        TCGA-DV-A4W0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-T7-A92I 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D82V10, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                10 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3451        TCGA-B2-A4SR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5550        TCGA-DV-A4W0        TCGA-G6-A8L7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-MM-A84U        TCGA-T7-A92I 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         5    38
  XQ LOSS WILD-TYPE     7                        51   419
D82V11, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               5                51
  WHITE                                  38               419
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  31
  XQ LOSS WILD-TYPE  26 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   31
  XQ LOSS WILD-TYPE   26  319
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              31               319
[1] 2 2
[1] FALSE
